Suffix tree searcher: exploration of common substrings in large DNA sequence sets

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dc.contributor.authorMinkley, David
dc.contributor.authorWhitney, Michael J
dc.contributor.authorLin, Song-Han
dc.contributor.authorBarsky, Marina G
dc.contributor.authorKelly, Chris
dc.contributor.authorUpton, Chris
dc.date.accessioned2015-05-19T19:43:01Z
dc.date.available2015-05-19T19:43:01Z
dc.date.copyright2014en_US
dc.date.issued2014-07-23
dc.descriptionBioMed Centralen_US
dc.description.abstractBackground: Large DNA sequence data sets require special bioinformatics tools to search and compare them. Such tools should be easy to use so that the data can be easily accessed by a wide array of researchers. In the past, the use of suffix trees for searching DNA sequences has been limited by a practical need to keep the trees in RAM. Newer algorithms solve this problem by using disk-based approaches. However, none of the fastest suffix tree algorithms have been implemented with a graphical user interface, preventing their incorporation into a feasible laboratory workflow. Results: Suffix Tree Searcher (STS) is designed as an easy-to-use tool to index, search, and analyze very large DNA sequence datasets. The program accommodates very large numbers of very large sequences, with aggregate size reaching tens of billions of nucleotides. The program makes use of pre-sorted persistent “building blocks” to reduce the time required to construct new trees. STS is comprised of a graphical user interface written in Java, and four C modules. All components are automatically downloaded when a web link is clicked. The underlying suffix tree data structure permits extremely fast searching for specific nucleotide strings, with wild cards or mismatches allowed. Complete tree traversals for detecting common substrings are also very fast. The graphical user interface allows theuser to transition seamlessly between building, traversing, and searching the dataset. Conclusions: Thus, STS provides a new resource for the detection of substrings common to multiple DNA sequences or within a single sequence, for truly huge data sets. The re-searching of sequence hits, allowing wild card positions or mismatched nucleotides, together with the ability to rapidly retrieve large numbers of sequence hits from the DNA sequence files, provides the user with an efficient method of evaluating the similarity between nucleotide sequences by multiple alignment or use of Logos. The ability to re-use existing suffix tree pieces considerably shortens index generation time. The graphical user interface enables quick mastery of the analysis functions, easy access to the generated data, and seamless workflow integration.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.description.sponsorshipThis work was funded by a Canadian NSERC Discovery grant to CU and by NIAID grant HHSN266200400036C.en_US
dc.identifier.citationMinkley et al.: Suffix tree searcher: exploration of common substrings in large DNA sequence sets. BMC Research Notes 2014 7:466en_US
dc.identifier.urihttp://www.biomedcentral.com/1756-0500/7/466
dc.identifier.urihttp://dx.doi.org/10.1186/1756-0500-7-466
dc.identifier.urihttp://hdl.handle.net/1828/6180
dc.language.isoenen_US
dc.publisherBMC Research Notesen_US
dc.rightsAttribution-NonCommercial-NoDerivs 2.5 Canada*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/2.5/ca/*
dc.subjectSuffix tree
dc.subjectGenome
dc.subjectSubstring
dc.subjectDNA sequence
dc.subjectSTS
dc.subject.departmentDepartment of Microbiology and Biochemistry
dc.subject.departmentDepartment of Biochemistry and Microbiology
dc.titleSuffix tree searcher: exploration of common substrings in large DNA sequence setsen_US
dc.typeArticleen_US

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