CompareTwoSequences: CompareTwoSequences Compare two AA sequences in a blast...

In 47Lies/isoformnspectRe: Companion package of a nextflow pipeline

Description

CompareTwoSequences Compare two AA sequences in a blast results

Usage

CompareTwoSequences(QuerySequence, SubjectSequence, QueryStart = 12)

Arguments

QuerySequence	The query sequence in the blast result file, the query sequence correspond to the sequence of the protein bank aligned to the knowned protein bank (Uniprot for example).
SubjectSequence	The subject sequence in the blast results file, the subject sequence correspond to the known protein (typically one of UNIPROT) on which the query have been aligned.
QueryStart	In the case where the matching part of the query do not beggin with its N-Term extremity.

Value

IRanges with metadata corresponding to the differences between the two sequences, SAAV, Insertion, Deletion

Examples

R_FilePath <- system.file("extdata",
 "blast_rescue.example.txt",
  package = "isoformnspectRe")
Rescue<-read.table(
 R_FilePath,
 header=TRUE,
 stringsAsFactors = FALSE)
CompareTwoSequences(
 as.vector(Rescue$QuerySequence[1]),
 as.vector(Rescue$SubjectSequence[1]),
 as.vector(Rescue$QueryStart[1]))

47Lies/isoformnspectRe documentation built on May 29, 2021, 3 p.m.