align_to_unip: Align protein segnent around the hotspot to the...

In peterblattmann/DominoEffect: Identification and Annotation of Protein Hotspot Residues

Align protein segnent around the hotspot to the UniProt/Swiss-Prot KB sequence.

Description

This function alignes the Ensembl protein region with a hotspot to the UniProt sequence. The Ensembl region encompasses 15 amino acids where the hotspot is in the middle. If the hotspot was at the protein start or end the region is still 15 amino acids long, but the hotspot position is shifted.

Usage

  align_to_unip(ens.seq, uni.seq, ensembl_mut_position)

Arguments

ens.seq	AAString object with the Ensembl protein sequence corresponding to the representative transcript.
uni.seq	AAString with the UniProt sequence for the identifier matching the Ensembl gene name.
ensembl_mut_position	Numeric vector defining the hotspot position in the Ensembl sequence, i.e. in the ens.seq

Value

Returns a list where the first element is a character vector defining whether there was a significant alignment and the second element provides the hotspot position in the UniProt sequence.

Author(s)

Marija Buljan <[e-mail]> Peter Blattmann <[e-mail]>

Examples

library(Biostrings)

ens.seq <- AAString("MDLSALREEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLK")
uni.seq <- AAString("MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLA")
ensembl_mut_position <- 25

align_to_unip(ens.seq, uni.seq, ensembl_mut_position)

peterblattmann/DominoEffect documentation built on Nov. 9, 2023, 2:39 a.m.