silic_tryp: silic_tryp function

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

silic_tryp performs silicon trypsination and returns the fragments to which the position coordinate points. The position value is corrected so that it afterwards points to the same amino-acid as before.

Usage

silic_tryp(seq,pos,id)

Arguments

seq	Character. Amino-acid sequences which are to be truncated.
pos	Numeric. Points to an amino-acid inside the sequence.
id	Numeric. An identifier which is copied to the result table.

Details

The routine implements the "Keil"-rule, where sites are described by the regex "[RK](?!P)". The cut position is between [RK] and the following character. The sequence fragment which contains the exon-intron boundary (depicted by position) is returned. Dependent numeric values are recalculated.

Value

data.frame

Author(s)

Wolfgang Kaisers

Examples

silic_tryp(seq="AXKUEMRFG",pos=4)

spliceSites documentation built on May 6, 2019, 3:05 a.m.