epitopefindr: epitopefindr: a package for identifying minimal overlaps from...
In brandonsie/epitopefindr: Minimal Overlaps from BLAST Alignments

Description Details

The purpose of this package is to describe the alignments among a set of peptide sequences by reporting the overlaps of each peptide's alignments to other peptides in the set. One can imagine inputting a list of peptides enriched by immunoprecipitation to identify corresponding epitopes.

'epitopefindr' takes a .fasta file listing peptide sequences of interest and calls BLASTp from within R to identify alignments among these peptides. Each peptide's alignments to other peptides are then simplified to the minimal number of "non overlapping" intervals* of the index peptide that represent all alignments to other peptides reported by BLAST. *By default, each interval must be at least 7 amino acids long, and two intervals are considered NOT overlapping if they share 6 or fewer amino acids. After the minimal overlaps are identified for each peptide, these overlaps are gathered into aligning groups based on the initial BLAST. For each group, a multiple sequence alignment logo, or motif, is generated to represent the collective sequence. Additionally, a spreadsheet is written to list the final trimmed amino acid sequences and some metadata.

brandonsie/epitopefindr documentation built on Oct. 31, 2021, 5:20 p.m.