epitopefindr: epitopefindr: a package for identifying minimal overlaps from...
In brandonsie/epitopefindr: Minimal Overlaps from BLAST Alignments
epitopefindr R Documentation
epitopefindr: a package for identifying minimal overlaps from BLAST alignments.
Description
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.
Details
'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 May 4, 2024, 10:27 a.m.
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| epitopefindr | R Documentation |
epitopefindr: a package for identifying minimal overlaps from BLAST alignments.
Description
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.
Details
'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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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