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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry. / Temu, Tikira; Mann, Matthias; Räschle, Markus; Cox, Jürgen.

In: Bioinformatics (Online), Vol. 32, No. 9, 01.05.2016, p. 1417-9.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Temu, T, Mann, M, Räschle, M & Cox, J 2016, 'Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry', Bioinformatics (Online), vol. 32, no. 9, pp. 1417-9. https://doi.org/10.1093/bioinformatics/btv756

APA

Temu, T., Mann, M., Räschle, M., & Cox, J. (2016). Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry. Bioinformatics (Online), 32(9), 1417-9. https://doi.org/10.1093/bioinformatics/btv756

Vancouver

Temu T, Mann M, Räschle M, Cox J. Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry. Bioinformatics (Online). 2016 May 1;32(9):1417-9. https://doi.org/10.1093/bioinformatics/btv756

Author

Temu, Tikira ; Mann, Matthias ; Räschle, Markus ; Cox, Jürgen. / Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry. In: Bioinformatics (Online). 2016 ; Vol. 32, No. 9. pp. 1417-9.

Bibtex

@article{94e449bffc4e453b9bd1b0a1d077db0a,
title = "Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry",
abstract = "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.deSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",
keywords = "Amino Acid Sequence, Animals, Base Sequence, High-Throughput Nucleotide Sequencing, Humans, Mass Spectrometry, Proteomics, Journal Article",
author = "Tikira Temu and Matthias Mann and Markus R{\"a}schle and J{\"u}rgen Cox",
note = "{\textcopyright} The Author 2016. Published by Oxford University Press.",
year = "2016",
month = may,
day = "1",
doi = "10.1093/bioinformatics/btv756",
language = "English",
volume = "32",
pages = "1417--9",
journal = "Bioinformatics (Online)",
issn = "1367-4811",
publisher = "Oxford University Press",
number = "9",

}

RIS

TY - JOUR

T1 - Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry

AU - Temu, Tikira

AU - Mann, Matthias

AU - Räschle, Markus

AU - Cox, Jürgen

N1 - © The Author 2016. Published by Oxford University Press.

PY - 2016/5/1

Y1 - 2016/5/1

N2 - 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.deSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - 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.deSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

KW - Amino Acid Sequence

KW - Animals

KW - Base Sequence

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - Mass Spectrometry

KW - Proteomics

KW - Journal Article

U2 - 10.1093/bioinformatics/btv756

DO - 10.1093/bioinformatics/btv756

M3 - Journal article

C2 - 26743511

VL - 32

SP - 1417

EP - 1419

JO - Bioinformatics (Online)

JF - Bioinformatics (Online)

SN - 1367-4811

IS - 9

ER -

ID: 186877587