Mercurial > repos > bgruening > glimmer_gene_calling_workflow
diff readme.rst @ 0:03f5132065e2 draft
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author | bgruening |
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date | Wed, 10 Jul 2013 15:37:59 -0400 |
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children | ad01b12e0a0c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Wed Jul 10 15:37:59 2013 -0400 @@ -0,0 +1,28 @@ +============================== +Glimmer3 gene calling workflow +============================== + +This Tool Shed Repository contains a workflow for the gene prediction of from a given nucleotide FASTA file. + +At first an interpolated context model (ICM) is build from a know set of genes, preferable from the closest relative available organism(s). In a following step this ICM model is used to predict genes on the second input. The output is a FASTA file with nucleotide sequences that is further converted to proteins sequences. + +To run that worflow glimmer_ und the EMBOSS_ suite is required. Both can be installed from the Tool Shed. + +.. _glimmer: http://www.cbcb.umd.edu/software/glimmer/ +.. _EMBOSS: http://emboss.sourceforge.net/ + +| A. L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007). + +EMBOSS: The European Molecular Biology Open Software Suite (2000) +Rice,P. Longden,I. and Bleasby,A. +Trends in Genetics 16, (6) pp276--277 + +************ +Availability +************ + +This workflow is available on the main Galaxy Tool Shed: +http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_gene_calling_workflow + +Development is being done here: +https://github.com/bgruening/galaxytools/workflows/glimmer3/