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Epitope Coverage Assessment Tool - Epicover

Purpose: Given a putative vaccine or antigen protein 'cocktail', or a set of such cocktails, and a test set of natural or background proteins, this tool will calculate the proportion of all epitope-length peptides in the test sequence set that are 'covered' (i.e., matched) by some peptide or peptides in each protein cocktail. Results are expressed as mean epitope-coverage over all test sequences.

Options include epitope length, the number of mismatches in each epitope to score (from zero to the maximum you set), and a rarity limit (epitope-length fragments occurring in fewer than this minimum number of sequences will be ignored).

Advanced options involve separately reporting results for subsets of the test protein set. You can provide a file of grouped sequence names [example of format] or you may request the program to group the sequences by looking at their names. These options can be combined.

Usage: Paste your amino acid sequences in the boxes below, or use the browse button to select files on your computer that contain sequences to upload. Inputs may be combined. Sequences with toggles may be used, and most common sequence formats are accepted.

Input
Use output from MakeVaccine tool
Provide a job number to access output from the Mosaic Vaccine Designer tool:
OR
Provide input sequences
Paste antigen protein sequence(s):
and/or upload as files:
Paste test set protein sequences:
and/or upload as files:
Options
Send results as an email instead of displaying in browser
(useful in case of a browser time-out):
Nominal epitope length:
Maximum amino acid mismatches to score (range from 0):
Minimum number of occurrences of a potential epitope
in viral protein set to consider for coverage:
Precision to use when reporting coverage: decimal places
Advanced Options
Upload file of grouped sequence names
Report on subsets defined according to first character(s) in sequence names


Related Programs

References

last modified: Wed Mar 14 09:19 2012


Questions or comments? Contact us at seq-info@lanl.gov.

 
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