NDLI: Reducing Folding Scenario Candidates in Pseudoknots Detection Using PLMM_DPSS Algorithm Integrated With Energy Filters

Content Provider	IEEE Xplore Digital Library
Author	Xiaolu Huang Ali, H.
Copyright Year	2007
Description	Author affiliation: Univ. of Nebraska at Omaha, Omaha (Xiaolu Huang; Ali, H.)
Abstract	Pseudoknots are important functional structures in RNA. Despite of numerous pseudoknot prediction tools, biologists still need a pseudoknot detection method with much higher sensitivity. We have previously developed the pseudoknot local motif model and dynamic partner sequence stacking (PLMMDPSS) algorithm which predicts short loop 2 pseudoknots with high sensitivity. Integrated with Mfold, PLMM_DPSS is capable of predicting both H-type and complicated type pseudoknots. In this study, we have developed PLMM_DPSS_SF Mfold_FF with the following modifications: the extension of the PLM model to include long loop 2 pseudoknots, the incorporation of overall folding energy calculation, recombination of non-overlapping pseudoknots within one sequence and two filters for higher specificity, The prediction results have shown that PLMM_DPSS_SF_Mfold_FF is more sensitive than other leading pseudoknot prediction tools and results in a low alternative folding number, and results also support the notion that some kinetic barriers may trap RNA folding in local minimums.
Starting Page	1299
Ending Page	1303
File Size	1895792
Page Count	5
File Format	PDF
ISBN	9781424415090
DOI	10.1109/BIBE.2007.4375735
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	Filters RNA Predictive models Computer science Stacking Prediction algorithms Kinetic theory Iterative algorithms Biological system modeling Tree data structures filter PLMM_DPSS algorithm pseudoknot prediction
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