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Positional Epitope Coverage Assessment Tool - Posicover

Purpose: This tool will calculate the proportion of all epitope-length peptides in a set of aligned viral or antigen protein sequences that are 'covered' (i.e., matched) by a peptide in each viral or antigen protein cocktail. Results are expressed as epitope-coverage over the position of test sequences.

Usage: Paste your protein sequences in the boxes below, or use the browse button to select files on your computer that contain sequence(s) to upload. Most common sequence formats are accepted. Toggle peptides are allowed in antigen protein or peptide cocktail.

Input
Provide a job # from
Mosaic Vaccine Designer:

(Only the antigen set is used. Provide the ALIGNED viral test set below)
AND/OR
Paste antigen protein set
or peptide cocktail:
(alignment not required)

[Sample Input]
upload more [ + ] antigen files
and/or upload antigen file(s):

Test set proteins
Paste ALIGNED test viral protein set:
[Sample Input]
or upload an ALIGNED test proteins file:
 

Options
Nominal epitope length:
Antigen counts to compute upper bounds: a comma- or white-space-delimited list ( e.g. 1,3-5,7 )
Plots to make                               
Hits in their natural positions
Misses in their natural positions
Hits and misses in their natural positions
Hits ranked by coverage
Misses ranked by coverage
N-mer coverage by positions
Ranked n-mer coverage
Alignment Thumbnail
N-mer coverage directly on alignment


Related Programs

References

last modified: Wed Mar 14 09:20 2012


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

 
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