NDLI: Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System

Content Provider	IEEE Xplore Digital Library
Author	Michal, S. Ivry, T. Schalit-Cohen, O. Sipper, M. Barash, D.
Copyright Year	2004
Abstract	We focus on finding a consensus motif of a set of homologous or functionally related RNA molecules. Recent approaches to this problem have been limited to simple motifs, require sequence alignment, and make prior assumptions concerning the data set. We use genetic programming to predict RNA consensus motifs based solely on the data set. Our system-dubbed GeRNAMo (Genetic programming of RNA Motifs)-predicts the most common motifs without sequence alignment and is capable of dealing with any motif size. Our program only requires the maximum number of stems in the motif and, if prior knowledge is available, the user can specify other attributes of the motif (e.g., the range of the motif's minimum and maximum sizes), thereby increasing both sensitivity and speed. We describe several experiments using either ferritin iron response element (IRE), signal recognition particle (SRP), or microRNA sequences showing that the most common motif is found repeatedly and that our system offers substantial advantages over previous methods.
Sponsorship	IEEE Computer Society
Page Count	15
File Size	4139197
Starting Page	596
Ending Page	610
File Format	PDF
ISSN	15455963
Volume Number	4
Issue Number	4
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-10-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	RNA Genetic programming Sequences Proteins Evolutionary computation Iron Cells (biology) Degradation Predictive models Stochastic processes
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

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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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