| GBA manager: an online tool for querying low-complexity regions in proteins. | |
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MedLine Citation:
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PMID: 20078398 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Abstract We developed GBA Manager, an online software that facilitates the Graph-Based Algorithm (GBA) we proposed in our earlier work. GBA identifies the low-complexity regions (LCR) of protein sequences. GBA exploits a similarity matrix, such as BLOSUM62, to compute the complexity of the subsequences of the input protein sequence. It uses a graph-based algorithm to accurately compute the regions that have low complexities. GBA Manager is a user friendly web-service that enables online querying of protein sequences using GBA. In addition to querying capabilities of the existing GBA algorithm, GBA Manager computes the p-values of the LCR identified. The p-value gives an estimate of the possibility that the region appears by chance. GBA Manager presents the output in three different understandable formats. GBA Manager is freely accessible at http://bioinformatics.cise.ufl.edu/GBA/GBA.htm . |
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Authors:
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Nirmalya Bandyopadhyay; Tamer Kahveci |
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Publication Detail:
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Type: Journal Article |
Journal Detail:
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Title: Journal of computational biology : a journal of computational molecular cell biology Volume: 17 ISSN: 1557-8666 ISO Abbreviation: J. Comput. Biol. Publication Date: 2010 Jan |
Date Detail:
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Created Date: 2010-01-18 Completed Date: 2010-03-29 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9433358 Medline TA: J Comput Biol Country: United States |
Other Details:
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Languages: eng Pagination: 73-7 Citation Subset: IM |
Affiliation:
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Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms Amino Acid Sequence Molecular Sequence Data Proteins / chemistry* Sequence Analysis, Protein / methods* Software* |
| Chemical | |
Reg. No./Substance:
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0/Proteins |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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