silic_tryp {spliceSites}R Documentation

silic_tryp function

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)

[Package spliceSites version 1.28.0 Index]