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Bioinformatics 2016 May 01;329:1417-9. doi: 10.1093/bioinformatics/btv756.
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Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry.

Temu T , Mann M , Räschle M , Cox J .

UNLABELLED: To enable mass spectrometry (MS)-based proteomic studies with poorly characterized organisms, we developed a computational workflow for the homology-driven assembly of a non-redundant reference sequence dataset. In the automated pipeline, translated DNA sequences (e.g. ESTs, RNA deep-sequencing data) are aligned to those of a closely related and fully sequenced organism. Representative sequences are derived from each cluster and joined, resulting in a non-redundant reference set representing the maximal available amino acid sequence information for each protein. We here applied NOmESS to assemble a reference database for the widely used model organism Xenopus laevis and demonstrate its use in proteomic applications. AVAILABILITY AND IMPLEMENTATION: NOmESS is written in C#. The source code as well as the executables can be downloaded from http://www.biochem.mpg.de/cox Execution of NOmESS requires BLASTp and cd-hit in addition. CONTACT: cox@biochem.mpg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PubMed ID: 26743511
PMC ID: PMC4848398
Article link: Bioinformatics

Species referenced: Xenopus laevis
Genes referenced: mpg

Article Images: [+] show captions
References [+] :
Hughes, Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. 1994, Pubmed, Xenbase