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Comparative Analysis of Splice Site Regions by Information Content
We have applied concepts from information theory for a comparative analysis of donor (gt) and acceptor (ag) splice site regions in the genes of five different organisms by calculating their mutual information content (relative entropy) over a selected block of nucleotides. A similar pattern that the...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054069/ https://www.ncbi.nlm.nih.gov/pubmed/17531798 http://dx.doi.org/10.1016/S1672-0229(07)60003-5 |
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author | Rekha, T. Shashi Mitra, Chanchal K. |
author_facet | Rekha, T. Shashi Mitra, Chanchal K. |
author_sort | Rekha, T. Shashi |
collection | PubMed |
description | We have applied concepts from information theory for a comparative analysis of donor (gt) and acceptor (ag) splice site regions in the genes of five different organisms by calculating their mutual information content (relative entropy) over a selected block of nucleotides. A similar pattern that the information content decreases as the block size increases was observed for both regions in all the organisms studied. This result suggests that the information required for splicing might be contained in the consensus of ~6–8 nt at both regions. We assume from our study that even though the nucleotides are showing some degrees of conservation in the flanking regions of the splice sites, certain level of variability is still tolerated, which leads the splicing process to occur normally even if the extent of base pairing is not fully satisfied. We also suggest that this variability can be compensated by recognizing different splice sites with different spliceosomal factors. |
format | Online Article Text |
id | pubmed-5054069 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-50540692016-10-14 Comparative Analysis of Splice Site Regions by Information Content Rekha, T. Shashi Mitra, Chanchal K. Genomics Proteomics Bioinformatics Article We have applied concepts from information theory for a comparative analysis of donor (gt) and acceptor (ag) splice site regions in the genes of five different organisms by calculating their mutual information content (relative entropy) over a selected block of nucleotides. A similar pattern that the information content decreases as the block size increases was observed for both regions in all the organisms studied. This result suggests that the information required for splicing might be contained in the consensus of ~6–8 nt at both regions. We assume from our study that even though the nucleotides are showing some degrees of conservation in the flanking regions of the splice sites, certain level of variability is still tolerated, which leads the splicing process to occur normally even if the extent of base pairing is not fully satisfied. We also suggest that this variability can be compensated by recognizing different splice sites with different spliceosomal factors. Elsevier 2006 2007-05-23 /pmc/articles/PMC5054069/ /pubmed/17531798 http://dx.doi.org/10.1016/S1672-0229(07)60003-5 Text en © 2006 Beijing Institute of Genomics http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/). |
spellingShingle | Article Rekha, T. Shashi Mitra, Chanchal K. Comparative Analysis of Splice Site Regions by Information Content |
title | Comparative Analysis of Splice Site Regions by Information Content |
title_full | Comparative Analysis of Splice Site Regions by Information Content |
title_fullStr | Comparative Analysis of Splice Site Regions by Information Content |
title_full_unstemmed | Comparative Analysis of Splice Site Regions by Information Content |
title_short | Comparative Analysis of Splice Site Regions by Information Content |
title_sort | comparative analysis of splice site regions by information content |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054069/ https://www.ncbi.nlm.nih.gov/pubmed/17531798 http://dx.doi.org/10.1016/S1672-0229(07)60003-5 |
work_keys_str_mv | AT rekhatshashi comparativeanalysisofsplicesiteregionsbyinformationcontent AT mitrachanchalk comparativeanalysisofsplicesiteregionsbyinformationcontent |