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LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences
Motivation: Local compositionally biased and low complexity regions (LCRs) in amino acid sequences have initially attracted the interest of researchers due to their implication in generating artifacts in sequence database searches. There is accumulating evidence of the biological significance of LCR...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481844/ https://www.ncbi.nlm.nih.gov/pubmed/25712690 http://dx.doi.org/10.1093/bioinformatics/btv115 |
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author | Kirmitzoglou, Ioannis Promponas, Vasilis J. |
author_facet | Kirmitzoglou, Ioannis Promponas, Vasilis J. |
author_sort | Kirmitzoglou, Ioannis |
collection | PubMed |
description | Motivation: Local compositionally biased and low complexity regions (LCRs) in amino acid sequences have initially attracted the interest of researchers due to their implication in generating artifacts in sequence database searches. There is accumulating evidence of the biological significance of LCRs both in physiological and in pathological situations. Nonetheless, LCR-related algorithms and tools have not gained wide appreciation across the research community, partly due to the fact that only a handful of user-friendly software is currently freely available. Results: We developed LCR-eXXXplorer, an extensible online platform attempting to fill this gap. LCR-eXXXplorer offers tools for displaying LCRs from the UniProt/SwissProt knowledgebase, in combination with other relevant protein features, predicted or experimentally verified. Moreover, users may perform powerful queries against a custom designed sequence/LCR-centric database. We anticipate that LCR-eXXXplorer will be a useful starting point in research efforts for the elucidation of the structure, function and evolution of proteins with LCRs. Availability and implementation: LCR-eXXXplorer is freely available at the URL http://repeat.biol.ucy.ac.cy/lcr-exxxplorer. Contact: vprobon@ucy.ac.cy Supplementary information: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-4481844 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-44818442015-06-30 LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences Kirmitzoglou, Ioannis Promponas, Vasilis J. Bioinformatics Applications Notes Motivation: Local compositionally biased and low complexity regions (LCRs) in amino acid sequences have initially attracted the interest of researchers due to their implication in generating artifacts in sequence database searches. There is accumulating evidence of the biological significance of LCRs both in physiological and in pathological situations. Nonetheless, LCR-related algorithms and tools have not gained wide appreciation across the research community, partly due to the fact that only a handful of user-friendly software is currently freely available. Results: We developed LCR-eXXXplorer, an extensible online platform attempting to fill this gap. LCR-eXXXplorer offers tools for displaying LCRs from the UniProt/SwissProt knowledgebase, in combination with other relevant protein features, predicted or experimentally verified. Moreover, users may perform powerful queries against a custom designed sequence/LCR-centric database. We anticipate that LCR-eXXXplorer will be a useful starting point in research efforts for the elucidation of the structure, function and evolution of proteins with LCRs. Availability and implementation: LCR-eXXXplorer is freely available at the URL http://repeat.biol.ucy.ac.cy/lcr-exxxplorer. Contact: vprobon@ucy.ac.cy Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2015-07-01 2015-02-20 /pmc/articles/PMC4481844/ /pubmed/25712690 http://dx.doi.org/10.1093/bioinformatics/btv115 Text en © The Author 2015. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Applications Notes Kirmitzoglou, Ioannis Promponas, Vasilis J. LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences |
title | LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences |
title_full | LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences |
title_fullStr | LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences |
title_full_unstemmed | LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences |
title_short | LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences |
title_sort | lcr-exxxplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481844/ https://www.ncbi.nlm.nih.gov/pubmed/25712690 http://dx.doi.org/10.1093/bioinformatics/btv115 |
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