Mutationmapper: a tool to aid the mapping of protein mutation data
There has been a rapid increase in the amount of mutational data due to, amongst other things, an increase in single nucleotide polymorphism (SNP) data and the use of site-directed mutagenesis as a tool to help dissect out functional properties of proteins. Many manually curated databases have been...
| Main Authors: | , |
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| Format: | Journal article |
| Language: | English |
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Public Library of Science
2013
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| _version_ | 1797065894470352896 |
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| author | Vohra, S Biggin, P |
| author_facet | Vohra, S Biggin, P |
| author_sort | Vohra, S |
| collection | OXFORD |
| description | There has been a rapid increase in the amount of mutational data due to, amongst other things, an increase in single nucleotide polymorphism (SNP) data and the use of site-directed mutagenesis as a tool to help dissect out functional properties of proteins. Many manually curated databases have been developed to index point mutations but they are not sustainable with the ever-increasing volume of scientific literature. There have been considerable efforts in the automatic extraction of mutation specific information from raw text involving use of various text-mining approaches. However, one of the key problems is to link these mutations with its associated protein and to present this data in such a way that researchers can immediately contextualize it within a structurally related family of proteins. To aid this process, we have developed an application called MutationMapper. Point mutations are extracted from abstracts and are validated against protein sequences in Uniprot as far as possible. Our methodology differs in a fundamental way from the usual text-mining approach. Rather than start with abstracts, we start with protein sequences, which facilitates greatly the process of validating a potential point mutation identified in an abstract. The results are displayed as mutations mapped on to the protein sequence or a multiple sequence alignment. The latter enables one to readily pick up mutations performed at equivalent positions in related proteins. We demonstrate the use of MutationMapper against several examples including a single sequence and multiple sequence alignments. The application is available as a web-service at http://mutationmapper.bioch.ox.ac.uk. |
| first_indexed | 2024-03-06T21:34:52Z |
| format | Journal article |
| id | oxford-uuid:45e0dcc7-19df-4cc7-98d8-bb09b4db39f3 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T21:34:52Z |
| publishDate | 2013 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | oxford-uuid:45e0dcc7-19df-4cc7-98d8-bb09b4db39f32022-03-26T15:10:32ZMutationmapper: a tool to aid the mapping of protein mutation dataJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:45e0dcc7-19df-4cc7-98d8-bb09b4db39f3EnglishSymplectic Elements at OxfordPublic Library of Science2013Vohra, SBiggin, PThere has been a rapid increase in the amount of mutational data due to, amongst other things, an increase in single nucleotide polymorphism (SNP) data and the use of site-directed mutagenesis as a tool to help dissect out functional properties of proteins. Many manually curated databases have been developed to index point mutations but they are not sustainable with the ever-increasing volume of scientific literature. There have been considerable efforts in the automatic extraction of mutation specific information from raw text involving use of various text-mining approaches. However, one of the key problems is to link these mutations with its associated protein and to present this data in such a way that researchers can immediately contextualize it within a structurally related family of proteins. To aid this process, we have developed an application called MutationMapper. Point mutations are extracted from abstracts and are validated against protein sequences in Uniprot as far as possible. Our methodology differs in a fundamental way from the usual text-mining approach. Rather than start with abstracts, we start with protein sequences, which facilitates greatly the process of validating a potential point mutation identified in an abstract. The results are displayed as mutations mapped on to the protein sequence or a multiple sequence alignment. The latter enables one to readily pick up mutations performed at equivalent positions in related proteins. We demonstrate the use of MutationMapper against several examples including a single sequence and multiple sequence alignments. The application is available as a web-service at http://mutationmapper.bioch.ox.ac.uk. |
| spellingShingle | Vohra, S Biggin, P Mutationmapper: a tool to aid the mapping of protein mutation data |
| title | Mutationmapper: a tool to aid the mapping of protein mutation data |
| title_full | Mutationmapper: a tool to aid the mapping of protein mutation data |
| title_fullStr | Mutationmapper: a tool to aid the mapping of protein mutation data |
| title_full_unstemmed | Mutationmapper: a tool to aid the mapping of protein mutation data |
| title_short | Mutationmapper: a tool to aid the mapping of protein mutation data |
| title_sort | mutationmapper a tool to aid the mapping of protein mutation data |
| work_keys_str_mv | AT vohras mutationmapperatooltoaidthemappingofproteinmutationdata AT bigginp mutationmapperatooltoaidthemappingofproteinmutationdata |