Blocked Pattern Matching Problem and Its Applications in Proteomics

Julio Ng, Amihood Amir, Pavel A. Pevzner

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

9 Scopus citations


Matching a mass spectrum against a text (a key computational task in proteomics) is slow since the existing text indexing algorithms (with search time independent of the text size) are not applicable in the domain of mass spectrometry. As a result, many important applications (e.g., searches for mutated peptides) are prohibitively time-consuming and even the standard search for non-mutated peptides is becoming too slow with recent advances in high-throughput genomics and proteomics technologies. We introduce a new paradigm – the Blocked Pattern Matching (BPM) Problem - that models peptide identification. BPM corresponds to matching a pattern against a text (over the alphabet of integers) under the assumption that each symbol a in the pattern can match a block of consecutive symbols in the text with total sum a. BPM opens a new, still unexplored, direction in combinatorial pattern matching and leads to the Mutated BPM (modeling identification of mutated peptides) and Fused BPM (modeling identification of fused peptides in tumor genomes). We illustrate how BPM algorithms solve problems that are beyond the reach of existing proteomics tools.

Original languageEnglish
Title of host publicationResearch in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings
EditorsVineet Bafna, S. Cenk Sahinalp
PublisherSpringer Verlag
Number of pages22
ISBN (Print)9783642200359
StatePublished - 2011
Event15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011 - Vancouver, BC, Canada
Duration: 28 Mar 201131 Mar 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6577 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011
CityVancouver, BC

Bibliographical note

Publisher Copyright:
© 2011, Springer-Verlag Berlin Heidelberg.


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