Difference between revisions of "Software for nematode research"
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Jump to navigationJump to search (New page: == Software Tools used by WormBase == *[http://stein.cshl.org/AcePerl/ AcePerl] *[http://www.gmod.org Generic Model Organism Database Project (GMOD)] *[http://www.bioperl.org BioPerl] ...) |
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| − | + | WormBase makes use of the following open-source software projects: | |
*[http://stein.cshl.org/AcePerl/ AcePerl] | *[http://stein.cshl.org/AcePerl/ AcePerl] | ||
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*[http://www.mysql.com MySQL] | *[http://www.mysql.com MySQL] | ||
*[http://www.textpresso.org Textpresso] - ''A text mining engine that powers the literature search'' | *[http://www.textpresso.org Textpresso] - ''A text mining engine that powers the literature search'' | ||
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| + | * [http://www.wormbook.org/chapters/www_webresourcesCelegans/webresourcesCelegans.html Web Resources for ''C. elegans''] - WormBook's WormMethod chapter by Raymond Lee containing core web resources for ''C. elegans'' research | ||
| + | * [http://elbrus.caltech.edu/cgi-bin/igor/motif_search/motif_search.cgi Motif Search] Search for DNA or protein motifs in ''C. elegans'' genome. | ||
| + | * [http://elbrus.caltech.edu/cgi-bin/igor/coexpression/profile.cgi Profile Search] Search for co-expressed genes using ''C. elegans'' microarray data. | ||
| + | * [http://elbrus.caltech.edu/cgi-bin/igor/go-cgi/go_mine.cgi GO Mine] Analyze frequency of GO terms in a list of genes or microarray probes. | ||
| + | * [http://elbrus.caltech.edu/cgi-bin/igor/microarraytools/dump_microarray_data_mysql.cgi Microarray Data Download] Download microarray data available in WormBase. | ||
| + | * [[Converting_Coordinates_between_releases|Converting Coordinates between releases]] Tool to help transform the coordinate of GFF files from one release to another | ||
| + | * [[Mapped Transgenes]] List of transgenes with known genomic locations. | ||
| + | * [[Tissue Specific Transgene Markers]] List of transgenes published as tissue specific markers. | ||
| + | * [[Balancers]] Table of Balancers from WormBook Chapter [http://www.wormbook.org/chapters/www_geneticbalancers/geneticbalancers.html Genetic Balancers] by Mark L. Edgley, David L. Baillie, Donald L. Riddle, and Ann M. Rose | ||
== Related projects and software tools == | == Related projects and software tools == | ||
*[http://www.bcgsc.ca/gc/bomge/sockeye/ Sockeye Genome Browser] | *[http://www.bcgsc.ca/gc/bomge/sockeye/ Sockeye Genome Browser] | ||
| + | *[http://genome.wustl.edu/genome/celegans/celegans_snp.cgi WUSTL SNP site] | ||
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| + | [[Category:Curation]] | ||
Latest revision as of 22:43, 16 August 2010
WormBase makes use of the following open-source software projects:
- AcePerl
- Generic Model Organism Database Project (GMOD)
- BioPerl
- ACeDB - The database engine that drives WormBase
- MySQL
- Textpresso - A text mining engine that powers the literature search
- Web Resources for C. elegans - WormBook's WormMethod chapter by Raymond Lee containing core web resources for C. elegans research
- Motif Search Search for DNA or protein motifs in C. elegans genome.
- Profile Search Search for co-expressed genes using C. elegans microarray data.
- GO Mine Analyze frequency of GO terms in a list of genes or microarray probes.
- Microarray Data Download Download microarray data available in WormBase.
- Converting Coordinates between releases Tool to help transform the coordinate of GFF files from one release to another
- Mapped Transgenes List of transgenes with known genomic locations.
- Tissue Specific Transgene Markers List of transgenes published as tissue specific markers.
- Balancers Table of Balancers from WormBook Chapter Genetic Balancers by Mark L. Edgley, David L. Baillie, Donald L. Riddle, and Ann M. Rose
