MetaMine – A tool to detect and analyse gene patterns in their environmental context
<p>Abstract</p> <p>Background</p> <p>Modern sequencing technologies allow rapid sequencing and bioinformatic analysis of genomes and metagenomes. With every new sequencing project a vast number of new proteins become available with many genes remaining functionally uncl...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-10-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/459 |
| _version_ | 1818551788302761984 |
|---|---|
| author | Kottmann Renzo Lombardot Thierry Bohnebeck Uta Glöckner Frank O |
| author_facet | Kottmann Renzo Lombardot Thierry Bohnebeck Uta Glöckner Frank O |
| author_sort | Kottmann Renzo |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Modern sequencing technologies allow rapid sequencing and bioinformatic analysis of genomes and metagenomes. With every new sequencing project a vast number of new proteins become available with many genes remaining functionally unclassified based on evidences from sequence similarities alone. Extending similarity searches with gene pattern approaches, defined as genes sharing a distinct genomic neighbourhood, have shown to significantly improve the number of functional assignments. Further functional evidences can be gained by correlating these gene patterns with prevailing environmental parameters. MetaMine was developed to approach the large pool of unclassified proteins by searching for recurrent gene patterns across habitats based on key genes.</p> <p>Results</p> <p>MetaMine is an interactive data mining tool which enables the detection of gene patterns in an environmental context. The gene pattern search starts with a user defined environmentally interesting key gene. With this gene a BLAST search is carried out against the Microbial Ecological Genomics DataBase (MEGDB) containing marine genomic and metagenomic sequences. This is followed by the determination of all neighbouring genes within a given distance and a search for functionally equivalent genes. In the final step a set of common genes present in a defined number of distinct genomes is determined. The gene patterns found are associated with their individual pattern instances describing gene order and directions. They are presented together with information about the sample and the habitat. MetaMine is implemented in Java and provided as a client/server application with a user-friendly graphical user interface. The system was evaluated with environmentally relevant genes related to the methane-cycle and carbon monoxide oxidation.</p> <p>Conclusion</p> <p>MetaMine offers a targeted, semi-automatic search for gene patterns based on expert input. The graphical user interface of MetaMine provides a user-friendly overview of the computed gene patterns for further inspection in an ecological context. Prevailing biological processes associated with a key gene can be used to infer new annotations and shape hypotheses to guide further analyses. The use-cases demonstrate that meaningful gene patterns can be quickly detected using MetaMine.</p> <p>MetaMine is freely available for academic use from <url>http://www.megx.net/metamine</url>.</p> |
| first_indexed | 2024-12-12T09:04:33Z |
| format | Article |
| id | doaj.art-4d8908e0719045658d830dddcf911654 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-12T09:04:33Z |
| publishDate | 2008-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-4d8908e0719045658d830dddcf9116542022-12-22T00:29:43ZengBMCBMC Bioinformatics1471-21052008-10-019145910.1186/1471-2105-9-459MetaMine – A tool to detect and analyse gene patterns in their environmental contextKottmann RenzoLombardot ThierryBohnebeck UtaGlöckner Frank O<p>Abstract</p> <p>Background</p> <p>Modern sequencing technologies allow rapid sequencing and bioinformatic analysis of genomes and metagenomes. With every new sequencing project a vast number of new proteins become available with many genes remaining functionally unclassified based on evidences from sequence similarities alone. Extending similarity searches with gene pattern approaches, defined as genes sharing a distinct genomic neighbourhood, have shown to significantly improve the number of functional assignments. Further functional evidences can be gained by correlating these gene patterns with prevailing environmental parameters. MetaMine was developed to approach the large pool of unclassified proteins by searching for recurrent gene patterns across habitats based on key genes.</p> <p>Results</p> <p>MetaMine is an interactive data mining tool which enables the detection of gene patterns in an environmental context. The gene pattern search starts with a user defined environmentally interesting key gene. With this gene a BLAST search is carried out against the Microbial Ecological Genomics DataBase (MEGDB) containing marine genomic and metagenomic sequences. This is followed by the determination of all neighbouring genes within a given distance and a search for functionally equivalent genes. In the final step a set of common genes present in a defined number of distinct genomes is determined. The gene patterns found are associated with their individual pattern instances describing gene order and directions. They are presented together with information about the sample and the habitat. MetaMine is implemented in Java and provided as a client/server application with a user-friendly graphical user interface. The system was evaluated with environmentally relevant genes related to the methane-cycle and carbon monoxide oxidation.</p> <p>Conclusion</p> <p>MetaMine offers a targeted, semi-automatic search for gene patterns based on expert input. The graphical user interface of MetaMine provides a user-friendly overview of the computed gene patterns for further inspection in an ecological context. Prevailing biological processes associated with a key gene can be used to infer new annotations and shape hypotheses to guide further analyses. The use-cases demonstrate that meaningful gene patterns can be quickly detected using MetaMine.</p> <p>MetaMine is freely available for academic use from <url>http://www.megx.net/metamine</url>.</p>http://www.biomedcentral.com/1471-2105/9/459 |
| spellingShingle | Kottmann Renzo Lombardot Thierry Bohnebeck Uta Glöckner Frank O MetaMine – A tool to detect and analyse gene patterns in their environmental context BMC Bioinformatics |
| title | MetaMine – A tool to detect and analyse gene patterns in their environmental context |
| title_full | MetaMine – A tool to detect and analyse gene patterns in their environmental context |
| title_fullStr | MetaMine – A tool to detect and analyse gene patterns in their environmental context |
| title_full_unstemmed | MetaMine – A tool to detect and analyse gene patterns in their environmental context |
| title_short | MetaMine – A tool to detect and analyse gene patterns in their environmental context |
| title_sort | metamine a tool to detect and analyse gene patterns in their environmental context |
| url | http://www.biomedcentral.com/1471-2105/9/459 |
| work_keys_str_mv | AT kottmannrenzo metamineatooltodetectandanalysegenepatternsintheirenvironmentalcontext AT lombardotthierry metamineatooltodetectandanalysegenepatternsintheirenvironmentalcontext AT bohnebeckuta metamineatooltodetectandanalysegenepatternsintheirenvironmentalcontext AT glocknerfranko metamineatooltodetectandanalysegenepatternsintheirenvironmentalcontext |