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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments
Bioinformatics, Volume 27, No. 17, Article btr417, Year 2011
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Description
Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Structure Predictor) is a program that takes into account thermodynamic stability, Boltzmann base pair probabilities, alignment uncertainty, covarying sites and evolutionary conservation to identify biologically relevant secondary structures within multiple sequence alignments. Unique to NASP is the consideration of all this information together with a recursive permutation-based approach to progressively identify and list the most conserved probable secondary structures that are likely to have the greatest biological relevance. By focusing on identifying only evolutionarily conserved structures, NASP forgoes the prediction of complete nucleotide folds but outperforms various other secondary structure prediction methods in its ability to selectively identify actual base pairings. © The Author 2011. Published by Oxford University Press. All rights reserved.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3157929/bin/supp_27_17_2443__index.html
https://efashare.b-cdn.net/share/pmc/articles/PMC3157929/bin/supp_btr417_Supplementary_figure_1.ppt
https://efashare.b-cdn.net/share/pmc/articles/PMC3157929/bin/supp_btr417_Supplementary_file_1.doc
Authors & Co-Authors
Semegni, J. Y.
South Africa, Cape Town
University of Cape Town
Wamalwa, Mark
South Africa, Bellville
University of the Western Cape
Gaujoux, Renaud
South Africa, Cape Town
University of Cape Town
Harkins, Gordon William
South Africa, Bellville
University of the Western Cape
Gray, A.
South Africa, Cape Town
University of Cape Town
Martin, Darren Patrick
South Africa, Cape Town
University of Cape Town
Statistics
Citations: 6
Authors: 6
Affiliations: 2
Identifiers
Doi:
10.1093/bioinformatics/btr417
ISSN:
13674803
e-ISSN:
14602059