NDLI: FastR: fast database search tool for non-coding RNA

Content Provider	IEEE Xplore Digital Library
Author	Bafna, V. Shaojie Zhang
Copyright Year	2004
Description	Author affiliation: Dept. of Comput. Sci. & Eng., California Univ., La Jolla, CA, USA (Bafna, V.; Shaojie Zhang)
Abstract	The discovery of novel non-coding RNAs has been among the most exciting recent developments in biology. Yet, many more remain undiscovered. It has been hypothesized that there is in fact an abundance of functional non-coding RNA (ncRNA) with various catalytic and regulatory junctions. Computational methods tailored specifically for ncRNA are being actively developed. As the inherent signal for ncRNA is weaker than that for protein coding genes, comparative methods offer the most promising approach, and are the subject of our research. We consider the following problem: Given an RNA sequence with a known secondary structure, efficiently compute all structural homologs (computed as a function of sequence and structural similarity) in a genomic database. Our approach, based on structural filters that eliminate a large portion of the database, while retaining the true homologs allows us to search a typical bacterial database in minutes on a standard PC, with high sensitivity and specificity. This is two orders of magnitude better than current available software for the problem.
Starting Page	52
Ending Page	61
File Size	329883
Page Count	10
File Format	PDF
ISBN	0769521940
DOI	10.1109/CSB.2004.1332417
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2004-08-19
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Sequences Filters Microorganisms Databases RNA Genomics Biology computing Sensitivity and specificity Bioinformatics
Content Type	Text
Resource Type	Article

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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
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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