Version 0.3 of SeqFeatR now available from CRAN.
The web-server uses version 0.3
SeqFeatR provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with features of the sequence.
For instance, given host HLA types (= features), SeqFeatR allows to identify viral immune escape mutations (= patterns).
Please cite:
Budeus B, Timm J, Hoffmann D (2016) SeqFeatR for the Discovery of Feature-Sequence Associations. PLoS ONE 11(1): e0146409.
How to use the tool:
Nucleotides Amino acids
Sequence alignment to analyse (FASTA):*
Download example input
Known epitopes (CSV):
Reference sequence (FASTA):
Known binding motifs (CSV):
One feature
HLA types
Position of feature HLA-A:* - -
Position of feature HLA-B:* - -
yes no
Height of horizontal line:
Height of star level:
Window size:
Fisher's exact test
Bayes Factor
Fixed Dirichlet precision parameter? yes no
Dirichlet precision parameter:
Minimal number of members:
P-value correction: none holm hochberg hommel bonferroni BH BY fdr
Check for phylogenetic bias? no yes
Show 'possible epitopes plot' (pdf)? yes no
Comment line for report sheet (max. 200 characters):
Your email-address:*
