PARPST: A PARallel algorithm to find peptide sequence tags

BMC Bioinformatics

Volumn 9, Issue SUPPL. 4, 2008, Pages

  Brunetti, Sara ^a   Lodi, Elena ^a   Mori, Elisa ^a   Stella, Maria ^a,b  

^a UNIVERSITY OF SIENA   (Italy)

^b NOVARTIS VACCINES AND DIAGNOSTICS   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL DATABASE; DATABASE SEARCHING; PEPTIDE SEQUENCE TAGS; PEPTIDE SEQUENCES; POST-TRANSLATIONAL MODIFICATIONS; PROTEIN IDENTIFICATION; SEQUENCE TAGS; TANDEM MASS SPECTROMETRY;

DATABASE SYSTEMS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PARALLEL ALGORITHMS; PEPTIDES; SEARCH ENGINES;

PARALLEL ARCHITECTURES;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; DATA ANALYSIS SOFTWARE; ESCHERICHIA COLI; EXPRESSED SEQUENCE TAG; NONHUMAN; PROTEIN DATABASE; PROTEIN PROCESSING; SEARCH ENGINE; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STRUCTURAL PROTEOMICS; CHEMISTRY; COMPUTER PROGRAM; MASS SPECTROMETRY; METHODOLOGY; MOLECULAR GENETICS; PEPTIDE MAPPING;

PEPTIDE;

ALGORITHMS; AMINO ACID SEQUENCE; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDE MAPPING; PEPTIDES; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 44649178730     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S4-S11     Document Type: Article

References (17)

1. Eng J McCormack A Yates J An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database Journal of American Society of Mass Spectrometry 1994, 5:976-989
2. Perkins D Pappin D Creasy D Cottrell J Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20:3551-3567 10612281
3. Bafna V Edwards N On de novo interpretation of tandem mass spectra for peptide identification Proceedings of the seventh annual international conference on Computational molecular biology: 10-30 April 2003; Berlin ACM Press Vingron M, Istrail S, Pevzner P, Waterman M 2003:9-18
4. Brunetti S Dutta D Liberatori L Mori E Varrazzo D An efficient algorithm for de novo peptide sequencing Proceeding of the seventh international conference on Adaptive and Natural Computing Algorithms: 21-23 March 2005; Coimbra Springer Verlag Ribeiro B, Albrecht RF, Dobnikar A, Pearson DW, Steele NC 2005:327-342
5. Brunetti S Lodi E Mori E De novo peptide sequencing: A work-efficient parallel algorithm Proceeding of the First International Conference on Bioinformatics Research and Development: 12-14 March 2007; Berlin OCG Hochreiter S, Küng J, Palkoska J, Wagner R 2007:66-67
6. Chen T Kao MK Tepel M Rush J Church GM A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms: 09-11 January 2000; San Francisco 2000:389-398
7. Danĉík V Addona TA Clauser KR Vath JE Pevzner PA De novo peptide sequencing via tandem mass spectrometry Journal of Computational Biology 1999, 6:327-342 10582570
8. Frank A Pevzner PA Pepnovo: De novo peptide sequencing via probabilistic network modeling Anal Chem 2005, 77:964-973 15858974
9. Lu B Chen T A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry Journal of Computational Biology 2003, 10:1-12 12676047
10. Ma B Zhang K Hendrie C Liang C Li M Doherty-Kirby A Lajoie G PEAKS: Powerful Software for Peptide De Novo Sequencing by MS/MS Rapid Communications in Mass Spectrometry 2003, 20:2337-2342
11. Mann M Wilm M Error-tolerant identification of peptides in sequence databases by peptide sequence tags Analytical Chemistry 1994, 66(24):4390-4399 7847635
12. Han Y Ma B Zhang K Spider: Software for protein identification from sequence tags with de novo sequencing error Journal of Bioinform. Comput. Biol. 2005, 3:697-716
13. Frank A Tanner S Bafna V Pevzner P Peptide sequence tags for fast database search in mass-spectrometry Journal of Proteome Research 2005, 4:1287-1295 16083278
14. Tabb DL Saraf A Yates JR Gutentag: High-throughput sequence tagging via an empirically derived fragmentation model Analytical Chemistry 2003, 23:415-6421
15. Liu C Yan B Song Y Xu Y Cai L Peptide sequence tag-based blind identification of post-translational modifications with point process model Bioinformatics 2006, 22:e307-e313 16873487
16. Jájá J An introduction to parallel algorithms Addison Wesley Longman Publishing Co.: Redwood City 1992
17. Prince JT Carlson MW Wang R Lu P Marcotte EM The need for a public proteomics repository Nat Biotechnol 2004, 22(4):471-472 15085804