Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry

Research output: Contribution to journalJournal articleResearchpeer-review

Tikira Temu, Matthias Mann, Markus Räschle, Jürgen Cox

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.

Original languageEnglish
JournalBioinformatics (Online)
Volume32
Issue number9
Pages (from-to)1417-9
Number of pages3
ISSN1367-4811
DOIs
Publication statusPublished - 1 May 2016
Externally publishedYes

    Research areas

  • Amino Acid Sequence, Animals, Base Sequence, High-Throughput Nucleotide Sequencing, Humans, Mass Spectrometry, Proteomics, Journal Article

ID: 186877587