This tool allows you to obtain all sequences (or a subset of sequences) which contain a selected region. Entries can be downloaded as Genbank records, or as alignments in FASTA or IG/Stanford format.

Note 1: Selecting the 5' LTR region will result in selecting sequences in both the 3' LTR and 5' LTR region. This problem will be corrected in the near future.

Note 2: Please check these alignments carefully before using them! Although they appear to be multiple alignments, they were not created by a program that considers all of the sequences while generating the alignment. Instead, alignments were created by a two-step process. First, the single sequence was aligned against a HMMER model. Second, gaps were inserted as needed to create the final product, an alignment of all sequences. While such alignments serve as a good starting point, they may not be optimal.

1. Search for sequences matching a name or accession number. Leaving both fields empty returns all sequences that match the other search criteria. Note: These are wild-card searches (see examples)

GenBank accession number: OR name:

Pre-defined region 5' LTR 5' LTR R 5' LTR U3 5' LTR U5 TAR Gag-Pol Gag p17 (matrix) p24 (capsid) p7 (nucleocapsid) p6 Pol CDS p51 (RT) p15 (RNAse H) p31 (integrase) protease Vif CDS Vpr CDS Tat CDS (includes intron) Tat exon 1 Tat exon 2 Rev CDS (includes intron) Rev exon 1 Rev exon 2 Vpu CDS Env CDS V1 V2 V3 V4 V5 RRE gp41 gp120 Nef CDS

User-defined range start: stop: (use the genome map above to choose the coordinates)
Subtype or CRF: ALL A B C D F (note: We are in the process of separating F into F1 and F2) F1 F2 G H J K L N O CRF01_AE CRF02_AG CRF03_AB CRF04_cpx CRF05_DF CRF06_cpx CRF07_BC CRF08_BC CRF10_CD CRF11_cpx CRF12_BF CRF13_cpx CRF14_BG Undefined Other (user defined)
Other Recombinant Subtype:
Isolation country: or geographic region ALL North America South America Central America Caribbean Oceania Middle-East Asia Africa Europe Former USSR Antarctica SubSaharan Africa Unknown
Isolation year:

3. Download only complete sequences, or include fragments of the specified region. If you choose to include partial sequences, you can set a minimum sequence length.

Limit to sequences that span the region
Include fragments. Minimum length:

4. You can either view the sequences in the web browser or download them.

View the sequences in your browser
Download the sequences to a PC
Download the sequences to a Macintosh
Download the sequences to a UNIX system

5. Choose the format for the sequences. If you choose IG or FASTA, the sequences will be aligned and you may clip the sequences to the region of interest (see #6 below). If you choose GenBank format, sequences will not be aligned, but you will get the background information concerning the sequence.

FASTA format (aligned)
STANFORD/IG format (aligned)
GENBANK format (NOT aligned)

6. If you are downloading an ALIGNED set of sequences in FASTA or IG format, you can have the sequences clipped down to the region of interest.

Clip to selected region
Show complete sequences (NOTE: these can be up 10.000 nucleotides long)

7. Choose the identification information for the sequences:

accession short_description (Genbank information)
subtype.country.isolation_year.common_name accession (NOTE: subtype and country are given if they are defined in our database. If common name is undefined, the GenBank locus is used instead)