HIV molecular immunology database

 

News Archive

2013 Alignments
The Web and Filtered Alignments are available online. 27 May 2014

RIP now accepts protein sequences
The Recombinant Identification Program (RIP) can now accept protein sequences as input. RIP can be used to identify viral subtypes and subtype recombinants. 30 April 2014

Variable Region Characteristics
Our new tool, Variable Region Characteristics, characterizes features within a peptide excised from a protein alignment, summarizing and reporting the following peptide characteristics: length, number of N-linked glycosylation sites. It is particularly useful for characterizing hypervariable regions in Env. 10 April 2014

CATNAP: Compile, Analyze, and Tally Neutralizing Antibody Panels
Our new tool, CATNAP compiles IC50 and IC80 neutralization panel data for HIV-1 broadly neutralizing antibodies. It provides tools for meta-analysis of neutralization panel data and viral Envelope sequences. 26 February 2014

HIV Genome Browser
Our new visualization tool, Genome Browser, is a customization of JBrowse designed to provide graphic views of the HIV genome and proteome. It incorporates many sources of data from the HIV Sequence and Immunology Databases, including epitopes, entropy, functional domains, and many features of interest. 26 February 2014

Alignment Slicer
Our new tool, Alignment Slicer, cuts vertical slices from any multiple sequence alignment. 21 November 2013

New BLAST download options
The HIV BLAST tool has new download options that allow you to download the HIV Database sequences of BLAST hits, aligned or unaligned, and to save BLAST results in a zip file. 19 November 2013

HIV Molecular Immunology 2013
HIV Molecular Immunology 2013 is now available online. The PDF version is hypertext enabled and features clickable table-of-contents, indexes, references and links to external web sites. 15 October 2013

Primer Design
This tool finds primers for PCR, sequencing (including NGS) and other molecular biology uses. It uses a multiple alignment and optimizes the primers to several user-defined criteria. 22 August 2013

Reference Sequence Coordinate Search
A new interface provides DNA coordinates for many features of the two reference sequences used by our database: HXB2 (HIV-1) and Mac239 (HIV-2 and SIV). 05 August 2013

HIV Sequence Compendium 2013
HIV Sequence Compendium 2013 is now available online. The printed copy is at the printers and should begin shipping in a few weeks. 01 August 2013

QuickAlign now works for any organism
Users can now input their own nucleotide or protein alignment in the QuickAlign tool. This expands the functionality of the tool for a variety of purposes, including non-HIV/SIV organisms. 15 July 2013

Sequence Compendium Subscriptions
The 2013 LANL HIV Sequence Compendium will be shipped later this summer. If you no longer need to receive a printed copy, or have changed your mailing address, please let us know. New subscribers are welcome. See: Compendium Subscriptions. 12 July 2013

GenBank Entry Generation
Our tool to prepare Sequin files for GenBank deposit has been expanded to include HIV-2 and SIV sequences. 19 June 2013

Broadly Neutralizing Antibody resources
Tables and a search interface provide detailed information about HIV-1 broadly neutralizing antibodies. 06 June 2013

2012 Alignments
The Web and Filtered Alignments are available online. 19 April 2013

Multiple input for HIV BLAST
HIV BLAST now accepts input of multiple sequences in a single run. 11 April 2013

Improvements for TreeRate
A new version of the TreeRate tool provides improved input options and clearer results for analysis of phylogenetic rates for trees with multi-timepoint sequence data. It also incorporates all functions of the former BranchLength tool. 06 March 2013

Sequence Locator improved output for multiple queries
For input of multiple sequences, Sequence Locator now provides links to download the summary information as tab-delimited text files of coordinates. 05 December 2012

New Options for Heatmap
The Heatmap tool produces a figure to visualize relations among numerical values in a data matrix, using either hierarchical or Kmeans clustering algorithms to group related values. Both methods now have new options for bootstrap resampling. 09 November 2012

HIV Molecular Immunology 2012
HIV Molecular Immunology 2012 is now available online. The PDF version is hypertext enabled and features clickable table-of-contents, indexes, references and links to external web sites. 10 October 2012

RIP update
The Recombinant Identification Program (RIP) has been updated to include more HIV-1 consensus sequences and circulating recombinant forms (CRFs). The RIP Explanation page now provides a background alignment that can be used to assay HIV-2 sequences. 20 September 2012

HIV Sequence Compendium 2012
HIV Sequence Compendium 2012 is now available on-line. The printed copy is at the printers and should begin shipping in a few weeks. 12 September 2012

PhyML Update
Our PhyML interface has been updated to version 3.0 and new options added. 10 September 2012

2011 Alignments
The Web and Filtered Alignments are available online. 06 September 2012

New Tool: Rainbow Tree
Rainbow Tree facilitates coloring branches in a phylogenetic tree coded according to labels included the sequences names (e.g. clade, country of origin, time point, patient...). 30 July 2012

Updated reference genome spreadsheet
The HXB2 Annotation spreadsheet is an Excel spreadsheet listing the HIV-1 subtype B molecular clone HXB2 reference sequence, with numbering of the nucleotide and amino acids positions, and sites of interest in the genome. This update adds the locations of the gp41 transmembrane domain, fusion peptide, N-helix and C-helix regions. 12 July 2012

New Option for Pixel
The Pixel tool provides quality control for alignments by color coding each residue in a graphical image. Two new color schemes allow the user to color the residues relative to the first sequence in the alignment, thus making some misalignments easier to see. 27 April 2012

Search Interface Amino Acid Options
The HIV Sequence Database now stores amino acid translations. The Search Interface now allows searches for amino acid motifs, and users can download aligned amino acid sequences in the correct reading frame. 26 April 2012

2011 Web Gene Alignments
The Web Gene Alignments are available online. 29 March 2012

New Features for Epitope Location Finder (ELF)
ELF displays known and predicted epitopes found within a protein sequence query. ELF results now include both Class I (CTL) and Class II (helper) epitopes. In addition to predicting epitopes based on anchor residues, ELF now includes predictions from the Class I and Class II Binding Predictions tools at the Immune Epitope Database (IEDB). 13 March 2012

New Features for HIV BLAST
HIV BLAST has new features. It now allows the user to find best matches among only subtyped sequences, or sequences of a specific subtype. It allows the resulting sequences to be downloaded fully aligned. 01 March 2012

New Option for N-GlycoSite
The N-GlycoSite tool predicts N-linked glycosylation sites in amino acid sequences. A new option allows the user to exclude sites with a second-position proline, which is disfavored for N-linked glycosylation. 29 February 2012

HIV Antibody Search Results More Specific
The antibody search interface in the HIV Immunology database is now more specific. Searches from the Author, Keyword, and Note fields now display only those notes and references that relate directly to the search. The user may still opt to display all, if desired 09 February 2012

New Options for Quickalign
The Quickalign tool aligns any short protein or nucleotide sequence with database sequences. New options provide additional ways to calculate and display frequency by position, and allow the user to include the surrounding region in the alignment. 08 February 2012

Next Generation Sequence Archive
We have established a repository for HIV, SIV and anti-HIV/SIV antibody ultradeep sequences. If you would like to add your data to the repository to make it available to the community, please contact us by email (see How to Submit on start page) to request write access. Submitted data can be freely downloaded. 08 December 2011

2010 Filtered Web Alignments
The Filtered Web Alignments are available online. 26 September 2011

2010 Alignments
The Web and Compendium Alignments are now available online. The Filtered Alignments will follow shortly. 07 September 2011

HIV Sequence Compendium 2011
HIV Sequence Compendium 2011 is now available on-line. The printed copy is at the printers and should begin shipping in a few weeks. 07 September 2011

Epitope Alignments
The HIV Molecular Immunology Database now features pre-built epitope alignments. The alignments consist of the unique epitope sequences aligned to the LANL HIV subtype reference alignments. 28 April 2011

Improved Immunology Search
Two features have been added to the HIV Molecular Immunology Database search interface. There is a new option to search by HXB2 location, and users may now control the strictness of the match in the search by epitope sequence field. 27 April 2011

GenBank Entry Generation
We have added a new tool that generates Sequin files for HIV-1 sequences. It provides an alternative to generating GenBank entries using the Quality Control tool. It will save time for users who do not need to perform the quality tests. The GenBank Entry Generation tool automatically generates HIV-1 protein annotations and includes them in the Sequin file. 23 February 2011

Poisson-Fitter
We have added a new tool that analyzes genetic data from early homogeneous HIV-1 samples and performs statistical tests on the Hamming Distance (HD) frequency distributions (Giorgi et al., BMC Bioinformatics 2010, 11:532). 17 November 2010

XLS Epitope Summaries
The Epitope Summary Tables are now available in XLS spreadsheet format. 02 November 2010

2009 Curated Alignments
The 2009 HIV-1, HIV-2 and SIV alignments are now available online. We have added new 'Filtered Web' alignments, which consist of a smaller number of sequences than the original web alignments. 13 July 2010

HIV Sequence Compendium 2010
HIV Sequence Compendium 2010 is now available on-line. The printed copy is at the printers and should begin shipping in a few weeks. 18 June 2010

Data Dictionary
For users who need detailed information about the structure of the HIV Sequence Database, we now provide a Data Dictionary. Each table and field of the sequence database is defined, with information about the data's source, type, and possible values. 12 May 2010

Cluster Fields
The HIV sequence database now contains database fields that identify sequences from epidemiologically-linked patients. These grouped patient IDs are termed "clusters" and represent groups of patients who share a virus of linked origin. The cluster fields can be searched from both the regular and advanced search interfaces. In the regular interface, look under "Patient information - More patient information". 06 May 2010

Sequence Compendium Subscriptions
The 2010 LANL HIV Sequence Compendium is being prepared and will be shipped in late May. If you no longer need to receive a printed copy, please help us conserve by unsubscribing. If you have changed your mailing address, please update it. New subscribers are welcome to sign up. You can modify subscription information here: Compendium Subscriptions. 20 April 2010

Next-gen HIV sequence archive
We have added an interface to download second-generation (mostly 454) HIV sequences that are stored in the NCBI SRA archive. Unfortunately the metadata associated with this archive is currently very limited, so we do not yet offer a search option. When the available information grows, we will add a search interface for these sequences. The interface has its own link under the "Search" header in the menu bar. 07 April 2010

Quality Control Tool
The QC tool analyzes HIV-1 nucleotide sequences to help identify a variety of problems. The tool compiles output from BLAST, RIP, TreeMaker, Gene Cutter, and HyperMut. The results are given in a user-friendly table, with links to more detailed output for each analysis. An optional second step can prepare HIV-1 sequence sets, together with related data, for submission to GenBank. 04 March 2010

Batch RIP
The RIP 3.0 viral subtyping tool can now accept multiple sequences at once. The results are returned by e-mail in a summary format. Links from the summary page lead to fully detailed results for each sequence. 23 February 2010

Quick link to NCBI's sequence viewer
We have added a quick link to view sequences retrieved using our search interface using the very nifty NCBI Sequence Viewer. The viewer shows the equivalent GenBank sequence, and therefore does not contain any of our added annotation. We hope to add this feature in the future. The link is accessible by clicking on the yellow- and-green icon that displays the sequence region in the search results. 07 January 2010

Erratum for HIV Sequence Compendium 2009
This erratum contains the correct HIV-1 Vpu alignment. The HIV Sequence Compendium 2009 erroneously contains a second copy of the Vif alignment instead of the Vpu alignment. 16 December 2009

HIV Molecular Immunology 2009
HIV Molecular Immunology 2009 is now available on-line. The PDF version is hypertext enabled and features `clickable' table-of-contents, indexes, references and links to external web sites. 15 September 2009

2009 Sequence Compendium
All subscribers to the Sequence Compendium should have received their 2009 copy by now. If you would like to stop receiving the printed compendium, or to change your mailing address, please send a message to seq-info@lanl.gov. Please include your name and address in all correspondence. 08 September 2009

Site unavailable Sat, 29 Aug 2009 7:00am-5:00pm MDT
Because of major electrical work beyond our control, www.hiv.lanl.gov and related sites will be unavailable on Saturday, 29 August 2009, 7:00am-5:00pm MDT (14:00-00:00 UTC). 26 August 2009

Geographic distribution of search results
With this new feature of our main search interface, you can display the results of your sequence search as a map, with pies to display the geographical origins of the sequences. Use the 'Geography' button on the search results page. 12 June 2009

ResDB is no longer available
Due to hardware failure we have had to take down the resistance mutation database. The data can still be downloaded from the site, as tab-delimited files. The entire website can also be downloaded, so you can locally restore the database. It requires MacOS9 and Filemaker Pro. 11 June 2009

Emails to China
Some email addresses in China appear to be unreachable from our server. One example is 163.com, but there are others. A temporary solution is to use a non-Chinese email address (gmail, yahoo, etc) instead. We are trying to solve the problem. 09 June 2009

HIV Sequence Compendium 2009
HIV Sequence Compendium 2009 is now available on-line. The printed copy is at the printers and should begin shipping in a few weeks. 22 May 2009

Sequence histograms
The output page of the HIV sequence Search Interface offers a new option, "Make Histogram". This option shows the distribution of your sequences across the HIV genome. At each position across the graph, the number of sequences overlapping that position is plotted as a bar. Colors within the bars represent different subtypes. The histogram allows you to see at a glance what regions and what subtypes are represented in your output. 08 April 2009

Better names for downloaded sequences
The search interface now gives the option of customizing the names of downloaded sequences. After clicking the "download sequences" button on the search results, click the "compose a label" link and choose the database fields to make up the sequence labels. This makes it possible to save some or all of the search information in the sequence names. 07 April 2009

TreeRate
We have released TreeRate, a web tool for re-rooting trees. Trees can be re-rooted using several methods including algorithms that optimize roots using single or multiple longitudinal samples. The intention of re-rooting the trees is to find the most homogeneous ("clocklike") evolutionary rate in the tree. Our previous tool Branchlength is now part of the TreeRate tool. 11 March 2009

RSS Feeds
The HIV Databases now offer the option to subscribe to RSS feeds. These RSS feeds will consist of all updates that appear in our News. 11 March 2009

Special Interest Alignments
A new page provides HIV sequence alignments and accompanying data of special interest to research. Each set of data consists of one or more DNA sequence alignments, references, and any accompanying data that are available. Sets are selected for inclusion based on availability and the likelihood that researchers will have an interest in using the data in other studies. Your help is needed to suggest or provide additional sets of data for inclusion. 11 March 2009

PepMap
New tool PepMap is available. The tool maps an input set of peptides on the HXB2 reference sequence, generates a table with peptide locations and peptide protein maps, similar to epitope maps. 23 February 2009

We have created a new Intra-patient Sequence Search interface (IPsearch). This interface is designed especially for retrieving longitudinal or other large intra-patient sequence sets. The interface is entirely functional, but will probably undergo small modifications over the coming weeks to optimize it. The link to it is in the 'Search' menu. 20 January 2009

We now provide an interface to PhyML, which generates much better trees than our simple Treemaker tool. The ML method is resource intensive, please try not to overload it. 16 January 2009

We migrated the HIV sequence database from Sybase to PostgreSQL. In the process we updated the Sequence Search Interface, the Advanced Search, the Geography Search Interface, and some minor tools associated with the database. 13 January 2009

Our page describing the Circulating Recombinant Forms (CRFs) has new images showing the subtypes in each recombinant more clearly. We have added an additional web page that lists the breakpoints for each CRF. 04 November 2008

We have a new tool called Pixel that visualizes large alignments as an image, using 1 pixel per residue. It can be very helpful when the alignments get large enough that you lose the overview, and quickly shows problems and misalignments. It works for both nucleotide and amino acid alignments. 25 October 2008

HIV Molecular Immunology 2008 is now available on-line. The PDF version is hypertext enabled and features `clickable' table-of-contents, indexes, references and links to external web sites. 13 August 2008

Updates for the 2008 Molecular Immunology Database now available on-line. Updated epitope maps and epitope summary tables are also on-line. 31 July 2008

The 2007 HIV-1, HIV-2/SIVsmm and PIV alignments are now available. The same webpage also has a new set of reference alignments. 09 July 2008

We have a new web tool, Heatmap. Heatmap is a web interface for analysis of quantitative data that may be particularly helpful for interpretations of immunological data, providing heat maps and hierarchical clustering. 26 June 2008

The Codon alignment tool can restore codons in your alignment so that the resulting alignment can be immediately translated. Currently this tool requires an input reading frame (or does its work for all 3 frames). In the future we will connect it to the reference sequence and the 'locate' tool so that it can find the correct reading frame automatically. 21 June 2008

Try out Phyloplace! This tool was designed to help users decide whether their sequence fits inside a currently known genotype subtype, or would be better classified as a new one. It can use either an intuitive distance-based method or the phylogenetic tree-based Branching index, and produces user-friendly graphical output for both. The tool also shows some promise for easily finding potential recombinants. 20 June 2008

We added a beta version of the new tool HIValign, which uses our HIV HMM alignment model to align user sequences. It can also codon-align the sequences, and separate individual HIV genes, and thus is a near-successor to Gene cutter. Please note that the tool has not yet been extensively tested. We would appreciate bug reports and other feedback. 19 June 2008

HIV Sequence Compendium 2008 is now available on-line. The printed copy is at the printers and should begin shipping in a few weeks. 05 June 2008

A link to jpHMM has been added to our Tools menu to make this subtyping/classification and recombination detection tool more accessible to the HIV community. This link currently goes to GOBICS (University of Goettingen) where it was developed together with the HIV Database team. A "local" version will be available soon. 22 March 2008

A beta version of a new tool, Protein Feature Accent, is now available. This user-friendly tool allows a user to highlight regions of interest on HIV protein structures. We will be adding features to this tool over the next few months, but the basics are in place. Suggestions for additional features are welcome. 21 March 2008

MOSAIC is a suite of related tools that can help in designing vaccine reagents, a web implementation of our vaccine design strategy for desiging full length mosaic proteins that give optimal potential epitope coverage.It assesses sequence diversity in terms of fragments of a specified length (e.g.9-mers, the length of a typical CTL epitope). Independent overall summaries of the number of perfect or close matches with the target sequence population can be obtained using Epicover, and levels of similarity spanning an alignment can be obtained with Posicover. 20 March 2008

The 14th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology will be held in Cape Town, South Africa, September 1-5, 2008. This workshop includes lectures and hands-on molecular bioinformatics training, in phylogenetic analyses and other types of genetic/protein sequence analysis. 19 March 2008

The 2006 HIV-1 web alignments are now available for download; the new HIV-2 and SIV alignments will follow shortly. We have also created a new download interface that gives access to all available alignments (web, subtype reference, and consensus/ancestral). This interface allows you to clip out a slice from the alignments if you provide the reference sequence coordinates. 25 February 2008

We have added a new tool called ElimDupes, for Eliminate Duplicates. It will take your alignment and remove duplicate sequences. Several options can be set, and the sequences can be automatically divided into groups (e.g. if there are data from several patients with multiple sequences each). In the future we will add an option to also remove sequences that are more than x% similar where x<=100. 29 January 2008

The Treemaker tool now lets you download your input sequences sorted in the order of the tree, which makes it much easier to select sequences in the alignment based on their phylogenetic behavior. 28 January 2008

The 15th HIV Dynamics and Evolution meeting will be in Santa Fe, NM, in April 27-30, 2008. Abstract deadline is February 15. It is organized by Thomas Leitner and Carla Kuiken. There will also be a pre-meeting at the Santa Fe Institute on recent developments in phylogenetic methods, organized by Bette Korber and Tanmoy Bhattacharya on April 27.
The HIV database will have two workshops at the HIV Keystone meeting in Banff, Canada, in March 27 - April 1, 2008. 23 January 2008

GeneCutter (sequence alignment and protein extraction tool) has been modified to return codon-aligned complete sequences in addition to aligned single proteins. Sequences spanning more than one protein are kept in frame by traversing a protein until it stops then switching to a overlapping protein reading frame. Go to GeneCutter. 02 November 2007

We will be making some infrastructural changes to the website in the coming week. This may break some links and bookmarks. We hope to minimize the impact, but please bear with us while we are at work. Please let us know of any problems at seq-info@lanl.gov. 31 October 2007

The HIV-1 Sequence Web Alignments are now available on-line. New HIV-2/SIVsmm and Other SIV alignments with be available on-line soon. 31 July 2007

HIV Sequence Compendium 2006/2007 is now available on-line in both pdf and html versions. The books are currently being printed and should begin shipping in a few weeks. 27 July 2007

HIV Molecular Immunology 2006/2007 is now available on-line. The PDF version is hypertext enabled and features `clickable' table-of-contents, indexes, references and links to external web sites. The printed copy is at the printers and should begin shipping in a few weeks. 17 July 2007

Updated CTL/CD8+ T-cell, T Helper/CD4+, and Antibody epitope summary tables are on-line. 27 April 2007

New tools for HLA Frequency Analysis. Graph HLA frequencies and search for linkage disequilibrium. 23 April 2007

Updated HIV Immunology epitope maps now available on-line for CTL, T helper and antibodies. 11 April 2007

The functionality of the "One seq/patient" button on the search interface has changed. Previously this would select all sequences associated with a patient, and then retain only one sequence for each patient; sequences without patient information were not selected. This has been changed: now this function selects all sequences except if there are more than one per patient. 05 April 2007

A beta version of the Quality Control / Genbank submission tool is now available to test. A QC submission runs several of our tools (GeneCutter, TreeMaker, Hypermut and RIP) on a sequence set and returns the results in an easy-to-read table. Results from this analysis will give a quick idea of whether there are problems or unexpected results with this set, for example undetected recombination, severe hypermutation, sequences that cluster in unexpected places (suggesting possible mislabeling) and stop codons that shouldn't be there. After going through QC, sequences can be prepared for submission to GenBank. Using this tool makes the submission process easier, and also allows you to include additional annotation information that Genbank doesn't easily accommodate, for example CD4 counts, HLA information, viral load, etc. The tool generates a Genbank submission file that can then be sent to Genbank, which will return the accession numbers. For problems or suggestions, please email us at seq-info@lanl.gov. 28 March 2007

As you can see, the HIV Sequence Database has a new look. This is not only a cosmetic change but hopefully also a more user-friendly version. We have put a lot of efforts into making tools and various information easier to find, pages more uniformly designed to enhance the intuitive use, and rewritten help pages with updated and clarified instructions. Please let us know if you have suggestions for further improvements. 30 January 2007

The old format converter, Seq-Convert, has been replaced by a new conversion program, Format Converter. This new converter is an in-house converter that can handle essentially all popular sequence formats. It is automatically applied in many of our tools so that users can input different formats and still get results. Now this converter is available as a stand alone tool for conversion of sequence files. 30 January 2007

An updated version of Hypermut 2.0 is now available. The new Hypermut interface can be customized to search for mutational patterns fitting any pattern desired. The new default pattern for detecting hypermutants is designed to detect hypermutational patterns induced by APOBEC3F or APOBEC3G. A publication describing all details of this new version is submitted and will be available as soon as possible. 30 January 2007

A new version of Treemaker is available. This version, similarly to the search interface tree building, allows the user to automatically include subtype reference sequences into a user provided alignment. Tree reconstruction is still made by neighbor joining, and models that are appropriate for HIV evolution are available. 30 January 2007

Updated CTL, CD8+ T-cell and Antibody epitope summary tables are on-line. 29 November 2006

The 2006 CTL, CD8+ T-cell and Antibody updates for the HIV Molecular Immunology Database now available on-line. 27 November 2006

A new website, Standardized Assessments of Neutralizing Antibodies for HIV/AIDS Vaccine Development is now available. This site provide papers, presentations, macros, links and documentation regarding David Montefiori's (Duke University) work on HIV reference strains for standard assessments of neutralizing antibodies for vaccine development. 20 November 2006

HIV-BLAST now allows users to enter their own set of sequences to use as the BLAST database. Previously, query sequences could only be blasted against the entire HIV database. This feature will be particularly useful when screening for lab contamination. 09 November 2006

The Principal Coordinates Analysis site PCOORD has been improved by the addition of options to strip gaps from the alignment and to apply either ID distances or Smith AA matrix. Protein and nucleotide alignments may be submitted and these are identified automatically. 27 September 2006

RIP3: We have released a completely new version of the recombinant identification program, RIP3. It's now a optimized fortran application that runs up to 10 times faster than RIP2. The default "consensus background" alignment has been totally reconstructed from the HIV database master complete genome alignment as has the "custom background". We have also refined the handling of gaps, and added a new feature that allows you flexibility in the scoring of IUPAC multistate characters that may be present in the query or background. Also new is an autosimplify function that winnows your initial RIP3 results to only the "best match" sequences, thus making the graphs and alignment more legible. In addition to the similarity plot the old RIP produced, graphs of Hamming distance and Jukes-Cantor distance are produced and may be downloaded in EPS, PS, or PNG format. The alignment output is now easier to read and includes position numbering both counting and not counting gaps. Give it a try at RIP3 Homepage 18 September 2006

We have a new update interface for users who would like to add their own epitopes or monoclonal antibodies to the HIV immunology database. If you have a new publication describing novel HIV immune responses, you can either enter the epitopes into the database, along with the citation, or alternatively unpublished results can be included with an author list. Entries will be reviewed by the immunology database staff, and entered into the database. While it can be difficult to publish a newly defined epitope, such epitopes can be useful to the larger research community, and we will put submission together annually as an epitope note so appropriate credit can be given for new unpublished contributions. Questions should be addressed to Bob Funkhouser, funkhouser@lanl.gov. 12 September 2006

A new web tool, the Recombinant HIV-1 Mapper, is now available. This site displays your recombinant breakpoint data for HIV-1 on a map of the HXB2 genome. The different subtypes that comprise your genome appear as colored regions in the map. 31 August 2006

A new tool to get colored overviews of alignments has been developed. This tool, Highlighter, lets you label mismatches or matches to multiple master sequences as well as resort the sequences. The mismatches can be considered as all mismatches, transition/ transversions or silent substitutions. The program allows IUPAC multistate characters. 13 July 2006

The Immune Epitope Database (IEDB) is available online. The IEDB is a project hosted at the La Jolla Institute for Allergy and Immunology (LIAI) that contains antibody and T cell epitope data curated from scientific literature and submitted from the community, as well as immunological analysis tools. 15 May 2006

Updated 2004 Web Alignments are now available on-line. The web alignments contain sequences received by the database up to and including 2004. 27 April 2006

Updated 2005 Subtype Reference Sequences are now available on-line. The updated reference set is used during tree-building by our search interface. A paper describing the criteria used in selecting the reference sequences is available online or as a pdf file. 02 February 2006

HIV Molecular Immunology 2005 is now available on-line. The PDF version is hypertext enabled and features `clickable' table-of-contents, indexes, references and links to external web sites. The printed copy is at the printers and should begin shipping in a few weeks. 17 January 2006

Please note the change in e-mail addresses: Use seq-info@lanl.gov instead of seq-info@t10.lanl.gov, and immuno@lanl.gov instead of immuno@t10.lanl.gov. 06 December 2005

Upcoming meetings: The 13th International Workshop on HIV Dynamics and Evolution will be held April 5 - 8, 2006 at the Marine Biology Labs, Woods Hole, Massachusetts. The HIV database group will present hands-on workshops at CROI 2006 in Denver, February 5-9, and at HIV Vaccines/Pathogenesis Keystone Meeting in Keystone, March 27 - April 2. 25 October 2005

Antibody updates for the 2004 Molecular Immunology Database now available on-line. Updated epitope maps and epitope summary tables are also on-line. 18 October 2005

A new search interface is now available that allows the user to directly align and analyze database search results, selected subtype reference sequences and aligned user sequences. This search and merge interface restricts the search results to the same start and stop HXB2 genome positions as in the user provided alignment. All other fields in the search interface will be active as in a normal search. The user can then either download the resulting alignment or build a phylogenetic tree. In case of building a tree, the user can also choose to add the subtype reference sequences and combine all three sets (user provided alignment, search results and subtype reference sequences) to build a tree. The tree is now calculated using PAUP* under several evolutionary models and can be downloaded or viewed in several formats. This new interface provides a quick way to analyze different molecular epidemiological questions. 22 September 2005

T Helper, CD4+, updates for the 2004 Molecular Immunology Database now available on-line. Updated epitope maps and epitope summary tables are also on-line. 03 August 2005

A new version of the gap removal tool is available. The new tool lets the user either remove all columns that include any gap symbol (strip) or only remove columns where all sequences have gaps (squeeze). 18 July 2005

CTL, CD8+ T-cell updates for the 2004 Molecular Immunology Database now available on-line. Updated epitope maps and epitope summary tables are also on-line. 08 June 2005

Gene Cutter has been updated with 2 significant changes: A reference sequence is no longer required in your sequence set, and unaligned sequences can be used as input. 08 June 2005

New sequence database search fields are available: viral load, CD4 and CD8 counts, ethnicity, and cohort. These field are poorly filled out at the moment, and this information is not available for most sequences, but over the next few years we will be striving to get this information whenever possible, particularly emphasizing large cohorts. A large data set from Durban South Africa is particularly well represented. 26 April 2005

A new screen enabling users to exclude problematic sequences has been added to the HIV sequence search interface. 30 March 2005

To avoid future confusion in CRF and subtype designations, the HIV nomenclature committee has agreed that for us to assign new CRF numbers or subtype letters we must be given the sequence and mosaic pattern maps of potentially new CRFs and subtypes before we can assign new names. See The Circulating Recombinant Forms. 25 January 2005

The 2003 HIV and SIV Sequence Alignments are now available online. 25 December 2004

The HIV Sequence Compendium 2003 is now available on-line. The printed copy is also being printed and shipped now. 17 December 2004

HIV Immunology and HIV/SIV Vaccine Databases 2003 is now available on-line. The PDF version is hypertext enabled and features `clickable' table-of-contents, indexes, references and links to external web sites. The printed copy is at the printers and should begin shipping in a few weeks. 17 November 2004

A beta version of an improved Gene Cutter has been posted. This version codon aligns HIV-1, HIV-2 and SIV alignments. It also has an improved output format. 27 October 2004

Antibody updates for the 2003 Molecular Immunology Database now available on-line. Updated epitope summary tables are also on-line. 27 October 2004

New 2003 antibody epitope maps now available on-line. 19 October 2004

RIP version 2.0 is now available. In this version the query sequence is automatically aligned to a reference set. The reference set can be chosen and modified by the user or inserted as in the old version 1. Additionally, there are now four different ways of plotting the window values. RIP 2.0 produces three output files: a graphical output, a tabular output of each position, and the resulting automatic alignment. 30 September 2004

The CTL and Helper sections of the HCV Immunology database are now online! 13 September 2004

30 June 2004

CTL, CD8+ T-cell updates for the 2003 Molecular Immunology Database now available on-line. Updated epitope maps and epitope summary tables are also on-line. 24 June 2004

The HIV/SIV Sequence Locator Tool now displays nucleotide coordinates when a protein sequence is submitted. It also displays the HXB2 nucleotides and amino acids equivalent to the submitted sequence. 04 June 2004

We have added a "summarize" function to Epilign which displays the different variants of your query epitope and their relative numbers in the alignment. 04 June 2004

We have redesigned our HIV Consensus Site. You can download up-to-date subtype consensuses for all the HIV subtypes here, or you can build your own consensuses using the new consensus tool. The consensus tool lets you set different thresholds for unanimity and majority, divide your alignment into blocks and automatically calculate a consensus for each block as well as a consensus-of-consensuses, and flexibly deal with gaps and non-standard characters. 04 June 2004

An updated version of the search interface is available. The new version maintains order across all operations and allows the download of selected records in tab-delimited format for easy processing in spreadsheet applications. 27 March 2004

Helper T cell updates for the 2003 Molecular Immunology Database now available on-line. Updated epitope maps and epitope summary tables are also on-line. 02 March 2004

29 February 2004

Files from the HIV Database Workshop given at 11th Conference on Retroviruses and Opportunistic Infections are available via ftp or http. 16 February 2004

Epitope Summary Tables are available for viewing and download. 14 February 2004

Class II data available for HLA Binding Motif Scanner (Motif Scan). 29 January 2004

Class II data available for HLA Binding Motif Scanner (Motif Scan). 29 January 2004

The web site is now searchable. 11 December 2003

The 2002 Sequence Alignments are now available. 30 November 2003

Improved versions of the Primalign and Sequence Locator tools are available. 20 November 2003

The Hepatitis C sequence database is now publicly accessible. It is based on the HIV database, and offers a similar set of tools, analysis options, and annotations. The two databases will post permanent links to each other's websites (see button above), and will share resources, tools and programs. An all-new HCV immunology database will become available in the winter or spring of 2004. 05 November 2003

New HLA Binding Motif Scanner (Motif Scan) version scans protein alignments. 21 October 2003

New HLA Typing and Epitope Mapping data sets now available. 20 October 2003

Files from the Workshop given at AIDS Vaccine 2003 are available here. 25 September 2003

New HLA Binding Motif Scanner (Motif Scan) now available. 08 September 2003

HIV Molecular Immunology 2002 is now available on-line. The PDF version is hypertext enabled and features `clickable' table-of-contents, indexes, references and links to external web sites. The printed copy is at the printers and should begin shipping in a few weeks. 08 August 2003

New 2002 Helper T cell epitope maps now available on-line. 07 August 2003

New 2002 CTL epitope maps now available on-line. 07 August 2003

HIV Database Workshops: The HIV database group is planning two hands-on computer workshops on Thursday, Sept. 18, 2003, to be held in conjunction with the AIDS Vaccine 2003 meeting in New York. The workshop will be free to those attending the conference. It will require advance registration . A program is currently available. Space will be limited to 20 participants per session. We will cover how to use the search and analysis tools provided through the HIV databases. Update: Registration will open Monday, August 11th at 9:00 am EST by calling 703-535-6863 15 July 2003

Helper T cell updates for the 2002 Molecular Immunology Database now available on-line. 19 June 2003

CTL updates for the 2002 Molecular Immunology Database now available on-line. 18 June 2003

An index to HIV protein and RNA 3D structures has been added. These web pages provide links to PDB structure entries, as well as links to tools for analyzing structures and tutorials and review articles on HIV protein and RNA 3D structures. 13 June 2003

New 2002 antibody epitope maps now available on-line. 19 May 2003

A redesigned HIV geography tool is available. This tool allows the user to have the HIV-1 subtype distribution plotted by region or by country. Subtypes and recombinants can be shown together or separately. The sequences and the frequency tables can be downloaded. In contrast to the old tool, the maps are updated daily. 18 May 2003

Glycosite highlights and tallies N-Linked Glycosylation sites in an aligned set of protein sequences. 07 May 2003

Antibody updates for the 2002 Molecular Immunology Database now available on-line. 29 April 2003

BLAST now accepts accession numbers as well as fasta sequences as input. 21 February 2003

Gene Cutter is a tool that clips pre-defined coding regions from a nucleotide alignment, then codon aligns and provides translations of the cut regions. 05 February 2003

We have a new version of the 'HXB2 numbering engine', called the 'HIV/SIV Sequence Locator Tool'. Improvements: the interface now accepts both amino acid and nucleotide sequences; it works for HIV-1, HIV-2, and SIV, and usually automatically recognizes which virus it is dealing with; it can process multiple submitted sequences; it can translate any CDS contained in the query to protein. 28 January 2003

We have a new sequence format conversion tool. Formats recognized are fasta, ig, msf, table, gcg, gde, slx and clustalw. 16 January 2003

We have a new HIV/SIV Vaccine Trials Database. The database contains trials published between 2000-2002 and some prior. This database is in Beta Test status. Complete data for each trial is not yet available. 19 December 2002

For the new Hepatitis C database group, we are looking for a postdoc to create and maintain the HCV immunology database, which will be the equivalent of the HIV immunology database. For more information and to apply, go here. 06 November 2002

We have updated and expanded the FAQ (Frequently Asked Questions). 09 October 2002

The subtype reference alignments have been updated. 19 September 2002

Upcoming meetings: 10th Conference on Retroviruses and Opportunistic Infections (February, 2003) and three Keystone Symposia (March-April, 2003) 03 September 2002

We have added new HIV-1, HIV-2, and SIV alignments. 30 August 2002

We have added new consensus and ancestral sequences for the M group and the subtypes to our alignments. 23 August 2002

Antibody updates for the 2001 Molecular Immunology Database now available on-line. 30 May 2002

New seach interface for Antibody immunology database. 30 May 2002

New 2001 antibody epitope maps now available on-line. 21 May 2002

Added link to sequence format conversion interface. 08 May 2002

New 2001 CTL epitope maps now available on-line. 06 March 2002

CTL updates for the 2001 Molecular Immunology Database now available on-line. 05 March 2002

New seach interface for CTL and Helper immunology databases. 05 March 2002

We have a improved search interface for the sequence database that combines the two previous search interfaces (HIVMAP and DBSearch). 05 March 2002

New 2001 Helper T cell epitope maps now available on-line. 13 February 2002

Helper T cell updates for the 2001 Molecular Immunology Database now available on-line. 11 February 2002

ELF the Epitope Location Finder tool is now available in beta-test version. 01 December 2001

Two more Circulating Recombinant Forms have been named: CRF13_cpx, consisting of subtypes A, E, G, J, U, and CRF14_BG. Their mosaic pattern can be found on the CRF page. 26 November 2001

The 9th International Workshop on HIV Dynamics and Evolution will be held March 17-20, 2002 at the UCLA Conference Center in Lake Arrowhead, California. 17 October 2001

The new sequence alignments are now available. 01 October 2001

The Molecular Immunology Database positions are now closed. 07 July 2001

PDF files of the complete 2000 HIV Molecular Immunology Compendium. 08 June 2001

Upcoming HIV meetings. 05 June 2001

Reviews from the 2000 HIV Molecular Immunology Compendium. 09 May 2001

Map overlapping peptides using PeptGen, with options to adjust length, overlap, and to exclude user selected amino acids from C- or N-terminal positions. Subtype consensus sequences available. 08 May 2001

New link: Protein prediction at Columbia University, a very versatile tool for protein structure prediction and several other analyses. On the "links" page. 05 April 2001

The new update for the geography pages is now up. 27 March 2001

An overview of HIV-1, HIV-2 and SIV subtype and CRF nomenclature is now available; this overview is accessible via the 'Tutorials' link, and will be kept up-to-date as new subtypes and CRFs are defined. 21 December 2000

An updated HLA Anchor residue motif scanner is now available to scan for possible epitopes in any protein. 13 December 2000

The Antibody Database has been updated with the new entries. 11 July 2000

The 1999 HIV Molecular Immunology compendium is now available online as PDF files. 07 July 2000

Our SeqPublish interface can now also be used to generate and download consensus sequences. 07 July 2000

The 1999 Human Retroviruses and AIDS compendium is now available online as pdf files. 05 July 2000

We have a job opening for a Graduate Research Assistant starting this fall. 22 June 2000

The new subtype reference alignments can be accessed via a HIV-MAP-like interface that allows you to clip out any region you need. 21 June 2000

Our interactive map-making tool is now available. The tool can be used to create geographical maps that show information on the relative and absolute frequency of HIV-1 subtypes by region. PLEASE NOTE: These frequencies reflect only the presence of each subtype in the database; because of extreme sampling bias, this need not be an accurate reflection of the actual prevalence of the subtypes in a region! 15 June 2000

New on the HIV Drug Resistance Website: Analyze resistance-related mutations with ADRA, our new Antiviral Drug-Resistance Analysis tool. 14 June 2000

We have created an overview of currently recognized Circulating Recombinant Forms (CRFs) including their mosaic patterns and representative sequences. 08 June 2000

The hypermutation detection interface has been updated. You can now investigate whether G-A hypermutation has resulted in stop codons, and view separate graphs for either dinucleotide context or all other mutations. 18 January 2000

Fragment tools. All our software for working with fragments, including newMotifscan (scans alignments for HLA binding motifs), newPrimalign (aligns nucleotide sequences against our alignments), Epilign, HXB2 numbering engine, SeqPublish, and newBLAST. 07 June 1999

HIV-BLAST Do a BLAST search of your sequence against the HIV database. 25 May 1999

The database search interface now has a field that allows searching by geographical region (e.g. Caribbean, Sub-saharan Africa, South America, etc). 21 May 1999

Finally! The long-awaited FAQ: Answers to all Frequently Asked Questions! 21 May 1999

We have invited a number of HIV experts to periodically evaluate our websites. We are very grateful for their help, and hope that the input of these web editors for the sequence and immunology pages will improve the usefulness of the site. 13 May 1999

Try out SeqPublish: submit your alignment and have it formatted for publication. 22 April 1999

The 1998 Sequence Compendium and Immunology Compendium can now be downloaded. 15 April 1999

Our website has been moved to a new (linux) machine. We hope this will lead to much faster response times, especially for database searches. 12 March 1999

The new alignments are now up. They are codon-aligned, and include almost all sequences in the database, while multiple sequences from a single individual were excluded. Also check out the new subtype reference alignments. 12 February 1999

We have a new database search interface! 22 January 1999

Statistics added to SNAP interface. The interface now calculates the variances and standard deviation for the average ds, dn, ps and pn values for the data set. 05 January 1999

Search for hypermutation in a dinucleotide context, using our new web interface. 19 November 1998

Standardized numbering system Find the HXB2 location corresponding to your primer, epitope, or sequence fragment; or find the HXB2 sequence corresponding to a position number. 13 November 1998

New SNAP interface that lets you analyze synonymous and nonsynonymous mutation rates without downloading the program SNAP. 19 October 1998

The Immunology Database is now searchable! Search for CTL, antibody, or helper epitopes, author names, and more. 23 September 1998

HMA gel analysis An interface to HDent and HDdist, programs for analysing data from heteroduplex mobility and tracking assays. 14 September 1998

New HIV-1 Sequence From Cameroon distinct from Groups M and O. 10 September 1998

Quality control in conserved regions Even if your region contains very little variation, there are ways to increase confidence in the validity of the sequences. 22 July 1998

Drug resistance database This database contains anti-HIV compounds, positions that are known to be associated with resistance, and references. 21 July 1998

ODprep/ODfit: These programs calculate antibody titers based on concentration and optical density data. 20 July 1998

SNAP - Synonymous Nonsynonymous Analysis Program. A program for comparing the rates of synonymous and nonsynonymous substitutions in a set of aligned sequences. 18 June 1998

PCOORD user interface An easy way to use the PCOORD program. 11 June 1998

Subtype reference alignments can be used to create a tree for subtyping a sequence. 10 June 1998

Search by region Select a region of the HIV genome, and retrieve the sequences that we have for this region. This page is still under construction. 08 June 1998

Sequence Quality Control Tools to make checking your sequences for contamination easy. 06 June 1998

Questions or comments? Contact us at immuno@lanl.gov
 
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