Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry
Research output: Contribution to journal › Journal article › Research › peer-review
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 language | English |
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Journal | Bioinformatics (Online) |
Volume | 32 |
Issue number | 9 |
Pages (from-to) | 1417-9 |
Number of pages | 3 |
ISSN | 1367-4811 |
DOIs | |
Publication status | Published - 1 May 2016 |
Externally published | Yes |
- Amino Acid Sequence, Animals, Base Sequence, High-Throughput Nucleotide Sequencing, Humans, Mass Spectrometry, Proteomics, Journal Article
Research areas
ID: 186877587