NDLI: An efficient data structure for applying multiple seeds in homology search

Content Provider	IEEE Xplore Digital Library
Author	Khodabakhshi, A.H. Mirzazadeh, M. Gupta, A.
Copyright Year	2007
Description	Author affiliation: Simon Fraser Univ., Burnaby (Khodabakhshi, A.H.)
Abstract	Homology search is a fundamental tool in genomics and proteomics research and considerable attention has been paid to the development of faster homology finding algorithms. The most efficient homology search algorithms known are based on finding short exact or near exact subsequences and then extending these to form long matches. Traditional tools such as FASTA and BLAST use the consecutive seed model, that is, an exact short match is found and then extended. More recently, PatternHunter, which uses the spaced seeds model, has shown considerably better sensitivity and attention has been focused on the design of optimal seeds for specific data sets. In some cases, the use of multiple seeds has been shown to be necessary. Here we focus on the problem of applying multiple seeds to a dataset in an efficient manner. In particular, when multiple seeds are applied, each seed can result in the same subsequence being found necessitating the removal of duplicates. We propose an efficient data structure that, given a set of seeds and two input sequences, reports the set of matching subsequences (that is, reports matching subsequences without duplications). We show that for any number of seeds, our algorithm is asymptotically optimal when the input sequences are longer than a certain threshold.
Starting Page	1374
Ending Page	1378
File Size	973010
Page Count	5
File Format	PDF
ISBN	9781424415090
DOI	10.1109/BIBE.2007.4375750
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-10-14
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Data structures Genomics Bioinformatics Databases Pattern matching Proteomics In vitro Robustness Genetic mutations Dynamic programming
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in