MAISTAS: a tool for automatic structural evaluation of alternative splicing products.

Handle URI:
http://hdl.handle.net/10754/596799
Title:
MAISTAS: a tool for automatic structural evaluation of alternative splicing products.
Authors:
Floris, Matteo; Raimondo, Domenico; Leoni, Guido; Orsini, Massimiliano; Marcatili, Paolo; Tramontano, Anna
Abstract:
MOTIVATION: Analysis of the human genome revealed that the amount of transcribed sequence is an order of magnitude greater than the number of predicted and well-characterized genes. A sizeable fraction of these transcripts is related to alternatively spliced forms of known protein coding genes. Inspection of the alternatively spliced transcripts identified in the pilot phase of the ENCODE project has clearly shown that often their structure might substantially differ from that of other isoforms of the same gene, and therefore that they might perform unrelated functions, or that they might even not correspond to a functional protein. Identifying these cases is obviously relevant for the functional assignment of gene products and for the interpretation of the effect of variations in the corresponding proteins. RESULTS: Here we describe a publicly available tool that, given a gene or a protein, retrieves and analyses all its annotated isoforms, provides users with three-dimensional models of the isoform(s) of his/her interest whenever possible and automatically assesses whether homology derived structural models correspond to plausible structures. This information is clearly relevant. When the homology model of some isoforms of a gene does not seem structurally plausible, the implications are that either they assume a structure unrelated to that of the other isoforms of the same gene with presumably significant functional differences, or do not correspond to functional products. We provide indications that the second hypothesis is likely to be true for a substantial fraction of the cases. AVAILABILITY: http://maistas.bioinformatica.crs4.it/.
Citation:
Floris M, Raimondo D, Leoni G, Orsini M, Marcatili P, et al. (2011) MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics 27: 1625–1629. Available: http://dx.doi.org/10.1093/bioinformatics/btr198.
Publisher:
Oxford University Press (OUP)
Journal:
Bioinformatics
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
15-Apr-2011
DOI:
10.1093/bioinformatics/btr198
PubMed ID:
21498402
PubMed Central ID:
PMC3106191
Type:
Article
ISSN:
1367-4803; 1460-2059
Sponsors:
King Abdullah University of Science and Technology (KAUST; Award No. KUK-I1-012-43); Fondazione Roma and the Italian Ministry of Health (contract no.onc_ord 25/07, FIRB ITALBIONET and PROTEOMICA).
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorFloris, Matteoen
dc.contributor.authorRaimondo, Domenicoen
dc.contributor.authorLeoni, Guidoen
dc.contributor.authorOrsini, Massimilianoen
dc.contributor.authorMarcatili, Paoloen
dc.contributor.authorTramontano, Annaen
dc.date.accessioned2016-02-21T08:50:55Zen
dc.date.available2016-02-21T08:50:55Zen
dc.date.issued2011-04-15en
dc.identifier.citationFloris M, Raimondo D, Leoni G, Orsini M, Marcatili P, et al. (2011) MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics 27: 1625–1629. Available: http://dx.doi.org/10.1093/bioinformatics/btr198.en
dc.identifier.issn1367-4803en
dc.identifier.issn1460-2059en
dc.identifier.pmid21498402en
dc.identifier.doi10.1093/bioinformatics/btr198en
dc.identifier.urihttp://hdl.handle.net/10754/596799en
dc.description.abstractMOTIVATION: Analysis of the human genome revealed that the amount of transcribed sequence is an order of magnitude greater than the number of predicted and well-characterized genes. A sizeable fraction of these transcripts is related to alternatively spliced forms of known protein coding genes. Inspection of the alternatively spliced transcripts identified in the pilot phase of the ENCODE project has clearly shown that often their structure might substantially differ from that of other isoforms of the same gene, and therefore that they might perform unrelated functions, or that they might even not correspond to a functional protein. Identifying these cases is obviously relevant for the functional assignment of gene products and for the interpretation of the effect of variations in the corresponding proteins. RESULTS: Here we describe a publicly available tool that, given a gene or a protein, retrieves and analyses all its annotated isoforms, provides users with three-dimensional models of the isoform(s) of his/her interest whenever possible and automatically assesses whether homology derived structural models correspond to plausible structures. This information is clearly relevant. When the homology model of some isoforms of a gene does not seem structurally plausible, the implications are that either they assume a structure unrelated to that of the other isoforms of the same gene with presumably significant functional differences, or do not correspond to functional products. We provide indications that the second hypothesis is likely to be true for a substantial fraction of the cases. AVAILABILITY: http://maistas.bioinformatica.crs4.it/.en
dc.description.sponsorshipKing Abdullah University of Science and Technology (KAUST; Award No. KUK-I1-012-43); Fondazione Roma and the Italian Ministry of Health (contract no.onc_ord 25/07, FIRB ITALBIONET and PROTEOMICA).en
dc.publisherOxford University Press (OUP)en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.5en
dc.subject.meshAlternative Splicingen
dc.subject.meshSoftwareen
dc.titleMAISTAS: a tool for automatic structural evaluation of alternative splicing products.en
dc.typeArticleen
dc.identifier.journalBioinformaticsen
dc.identifier.pmcidPMC3106191en
dc.contributor.institutionCenter for Advanced Studies, Research and Development in Sardinia, Pula, Italyen
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
kaust.grant.numberKUK-I1-012-43en

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