Publication: Stretch Profile: A pruning technique to accelerate DNA sequence search
Submitted Date
Received Date
Accepted Date
Issued Date
2020
Copyright Date
Announcement No.
Application No.
Patent No.
Valid Date
Resource Type
Edition
Resource Version
Language
en
File Type
No. of Pages/File Size
ISBN
ISSN
2352-9148
eISSN
Scopus ID
WOS ID
Pubmed ID
arXiv ID
item.page.harrt.identifier.callno
Other identifier(s)
Journal Title
Informatics in Medicine Unlocked
Volume
19
Issue
2020; 100323
Edition
Start Page
End Page
Access Rights
Access Status
Rights
Rights Holder(s)
Physical Location
Bibliographic Citation
Research Projects
Organizational Units
Authors
Journal Issue
Title
Stretch Profile: A pruning technique to accelerate DNA sequence search
Alternative Title(s)
Author's E-mail
Editor(s)
Editor’s Affiliation
Corresponding person(s)
Creator(s)
Compiler
Advisor(s)
Illustrator(s)
Applicant(s)
Inventor(s)
Issuer
Assignee
Other Contributor(s)
Series
Has Part
Abstract
DNA sequence similarity search has been used by scientists to facilitate biological research. Over the years; more sequences are added to databases; making them constantly larger. Existing sequence search techniques usually focus on the improvement of sequence search algorithms to make the search faster; ignoring the possibility of reducing unrelated sequences from the search. This paper presents a pruning technique to accelerate DNA sequence search based on a novel Stretch Profile created from stretches of consecutive base characters: A-Stretch; C-Stretch; G-Stretch; and T-Stretch. The Stretch Profile is pre-generated for each sequence in a sequence database. During the search; the Stretch Profile of the query sequence is generated for comparison. The sequences in the database whose profiles do not match the Stretch Profile of the query sequence are excluded from the search; resulting in the reduction of search space; and consequently; search time. For evaluation; we compare sequence retrievals from the Greengenes database and processing time when using only BLAST and when using the proposed pruning technique with BLAST. The results show that the proposed pruning technique can reduce the search time by 30.43% up to 63.74% depending on the length of input query; while maintaining a sensitivity of 1.00 when compared to the result of the original BLAST search.