NDLI: SEAL: a divide-and-conquer approach for sequence alignment

Content Provider	Springer Nature Link
Author	Kandadi, Harini Aygün, Ramazan Savas
Copyright Year	2015
Abstract	Sequence similarity search and sequence alignment methods are fundamental steps in comparative genomics and have a wide spectrum of application in the field of medicine, agriculture, and environment. The dynamic programming sequence alignment methods produce optimal alignments but are impractical for a similarity search due to their large running time. Heuristic methods like BLAST run much faster but may not provide optimal alignments. In this paper, we introduce a novel sequence alignment algorithm, SEAL. SEAL is a parallelizable algorithm that does not require gap penalty parameter as in heuristic methods. SEAL uses a combination of divide-and-conquer paradigm and the maximum contiguous subarray solution. SEAL is also improved by the use of borders in every contiguous segment. The alignment scores obtained by SEAL are consistently higher than those obtained by heuristic methods. Since the dependencies are minimized among intermediate steps, the complexity of SEAL can be reduced to $$\theta \,\left( {\log^{2} n} \right)$$ in the presence of satisfactory number of parallel processors.
Starting Page	1
Ending Page	11
Page Count	11
File Format	PDF
ISSN	21926662
Journal	Network Modeling Analysis in Health Informatics and Bioinformatics
Volume Number	4
Issue Number	1
e-ISSN	21926670
Language	English
Publisher	Springer Vienna
Publisher Date	2015-08-23
Publisher Place	Vienna
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Computational Biology/Bioinformatics Complex Networks Health Informatics Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Urology

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

An integrated algorithm for local sequence alignment

Biomedical and Health Informatics (BIH) workshop 2011

Mining clinical text for stroke prediction

Finding objects for assisting blind people

Positive unlabeled learning for deriving protein interaction networks

Algorithms for global protein–protein interaction network alignment

Erratum to: Mining clinical text for stroke prediction

Detecting signage and doors for blind navigation and wayfinding

Multiple networks modules identification by a multi-dimensional Markov chain method

SEAL: a divide-and-conquer approach for sequence alignment

Similar Documents

An integrated algorithm for local sequence alignment

Biomedical and Health Informatics (BIH) workshop 2011

Mining clinical text for stroke prediction

Finding objects for assisting blind people

Positive unlabeled learning for deriving protein interaction networks

Algorithms for global protein–protein interaction network alignment

Erratum to: Mining clinical text for stroke prediction

Detecting signage and doors for blind navigation and wayfinding

Multiple networks modules identification by a multi-dimensional Markov chain method

SEAL: a divide-and-conquer approach for sequence alignment