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A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs

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dc.contributor.author Zawaira, A
dc.contributor.author Shibayama, Y
dc.date.accessioned 2014-04-29T06:54:10Z
dc.date.available 2014-04-29T06:54:10Z
dc.date.issued 2012-12
dc.identifier.citation Zawaira, A and Shibayama, Y. 2012. A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs. J Struct Funct Genomics, vol. 13(4), pp 185-200 en_US
dc.identifier.issn 1345-711X
dc.identifier.uri http://download.springer.com/static/pdf/52/art%253A10.1007%252Fs10969-012-9141-7.pdf?auth66=1398588008_54b9d5387699d18617767a2405e199df&ext=.pdf
dc.identifier.uri http://hdl.handle.net/10204/7376
dc.description Copyright: 2012 Springer Verlag. This an ABSTRACT ONLY. The definitive version is published in J Struct Funct Genomics, vol. 13(4), pp 185-200 en_US
dc.description.abstract The study of the protein-protein interactions (PPIs) of unique ORFs is a strategy for deciphering the biological roles of unique ORFs of interest. For uniform reference, we define unique ORFs as those for which no matching protein is found after PDB-BLAST search with default parameters. The uniqueness of the ORFs generally precludes the straightforward use of structure-based approaches in the design of experiments to explore PPIs. Many open-source bioinformatics tools, from the commonly-used to the relatively esoteric, have been built and validated to perform analyses and/or predictions of sorts on proteins. How can these available tools be combined into a protocol that helps the non-expert bioinformaticist researcher to design experiments to explore the PPIs of their unique ORF? Here we define a pragmatic protocol based on accessibility of software to achieve this and we make it concrete by applying it on two proteins-the ImuB and ImuA' proteins from Mycobacterium tuberculosis. The protocol is pragmatic in that decisions are made largely based on the availability of easy-to-use freeware. We define the following basic and user-friendly software pathway to build testable PPI hypotheses for a query protein sequence: PSI-PRED MUSTER metaPPISP ASAView and ConSurf. Where possible, other analytical and/or predictive tools may be included. Our protocol combines the software predictions and analyses with general bioinformatics principles to arrive at consensus, prioritised and testable PPI hypotheses. en_US
dc.language.iso en en_US
dc.publisher Springer Verlag en_US
dc.relation.ispartofseries Workflow;10585
dc.subject Functional genomics en_US
dc.subject Sequence similarity en_US
dc.subject Sequence identity en_US
dc.subject Homology en_US
dc.subject Fold recognition en_US
dc.subject Protein interface en_US
dc.title A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs en_US
dc.type Article en_US


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