Species-specific analysis of protein sequence motifs using mutual information
<p>Abstract</p> <p>Background</p> <p>Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative des...
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| Format: | Article |
| Language: | English |
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BMC
2005-06-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/6/164 |
| _version_ | 1818118778963099648 |
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| author | Weckwerth Wolfram Keshvari Nima Hummel Jan Selbig Joachim |
| author_facet | Weckwerth Wolfram Keshvari Nima Hummel Jan Selbig Joachim |
| author_sort | Weckwerth Wolfram |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions. Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and, in particular, evolutionary features of the underlying sequences.</p> <p>Results</p> <p>We describe the tool <b><it>PRO</it></b><it>file analysis based on </it><b><it>M</it></b><it>utual </it><b><it>I</it></b><it>nformation </it>(PROMI) that enables comparative analysis of user-classified protein sequences. PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side. On the client-side platform-independence is achieved by generally applied internet delivery standards. As one possible application analysis of the zinc finger C<sub>2</sub>H<sub>2</sub>-type protein domain is introduced to illustrate the functionality of the tool.</p> <p>Conclusion</p> <p>The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences. It is available at <url>http://promi.mpimp-golm.mpg.de</url> where additional documentation can be found.</p> |
| first_indexed | 2024-12-11T04:59:43Z |
| format | Article |
| id | doaj.art-c78c82905d6443b683fc4012a6b7ef4f |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T04:59:43Z |
| publishDate | 2005-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-c78c82905d6443b683fc4012a6b7ef4f2022-12-22T01:20:11ZengBMCBMC Bioinformatics1471-21052005-06-016116410.1186/1471-2105-6-164Species-specific analysis of protein sequence motifs using mutual informationWeckwerth WolframKeshvari NimaHummel JanSelbig Joachim<p>Abstract</p> <p>Background</p> <p>Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions. Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and, in particular, evolutionary features of the underlying sequences.</p> <p>Results</p> <p>We describe the tool <b><it>PRO</it></b><it>file analysis based on </it><b><it>M</it></b><it>utual </it><b><it>I</it></b><it>nformation </it>(PROMI) that enables comparative analysis of user-classified protein sequences. PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side. On the client-side platform-independence is achieved by generally applied internet delivery standards. As one possible application analysis of the zinc finger C<sub>2</sub>H<sub>2</sub>-type protein domain is introduced to illustrate the functionality of the tool.</p> <p>Conclusion</p> <p>The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences. It is available at <url>http://promi.mpimp-golm.mpg.de</url> where additional documentation can be found.</p>http://www.biomedcentral.com/1471-2105/6/164 |
| spellingShingle | Weckwerth Wolfram Keshvari Nima Hummel Jan Selbig Joachim Species-specific analysis of protein sequence motifs using mutual information BMC Bioinformatics |
| title | Species-specific analysis of protein sequence motifs using mutual information |
| title_full | Species-specific analysis of protein sequence motifs using mutual information |
| title_fullStr | Species-specific analysis of protein sequence motifs using mutual information |
| title_full_unstemmed | Species-specific analysis of protein sequence motifs using mutual information |
| title_short | Species-specific analysis of protein sequence motifs using mutual information |
| title_sort | species specific analysis of protein sequence motifs using mutual information |
| url | http://www.biomedcentral.com/1471-2105/6/164 |
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