YMap: an Automated Method to Map Yeast Variants to Protein Modifications and Functional Regions

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2016 Nov 1

PMID 27797766

Authors

Ahmed Arslan

Vera van Noort

Affiliations

Soon will be listed here.

Abstract

Summary: Recent advances in sequence technology result in large datasets of sequence variants. For the human genome, several tools are available to predict the impact of these variants on gene and protein functions. However, for model organisms such as yeast such tools are lacking, specifically to predict the effect of protein sequence altering variants on the protein level. We present a python framework that enables users to map in a fully automated fashion large set of variants to protein functional regions and post-translationally modified residues. Furthermore, we provide the user with the possibility to retrieve predicted functional information on modified residues from other resources for example that are predicted to play a role in protein-protein interactions. The results are complemented by statistical tests to highlight the significance of underlying functions and pathways affected by mutations. We show the application of this package on a yeast dataset derived from a recent evolutionary experiment on adaptation to ethanol.

Availability And Implementation: The package is available from https://github.com/CSB-KUL/yMap and is implemented in Python.

Contact: vera.vannoort@biw.kuleuven.be.

Supplementary Information: Supplementary data are available at Bioinformatics online.

References

Cherry J . The Saccharomyces Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015; 2015(12):pdb.top083840. PMC: 5673599. DOI: 10.1101/pdb.top083840. View

Beltrao P, Albanese V, Kenner L, Swaney D, Burlingame A, Villen J . Systematic functional prioritization of protein posttranslational modifications. Cell. 2012; 150(2):413-25. PMC: 3404735. DOI: 10.1016/j.cell.2012.05.036. View

Stark C, Breitkreutz B, Reguly T, Boucher L, Breitkreutz A, Tyers M . BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2005; 34(Database issue):D535-9. PMC: 1347471. DOI: 10.1093/nar/gkj109. View

Minguez P, Letunic I, Parca L, Bork P . PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. Nucleic Acids Res. 2012; 41(Database issue):D306-11. PMC: 3531129. DOI: 10.1093/nar/gks1230. View

Adzhubei I, Schmidt S, Peshkin L, Ramensky V, Gerasimova A, Bork P . A method and server for predicting damaging missense mutations. Nat Methods. 2010; 7(4):248-9. PMC: 2855889. DOI: 10.1038/nmeth0410-248. View