Mercurial > repos > bgruening > glimmer_gene_calling_workflow
comparison 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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| 1 ============================== | |
| 2 Glimmer3 gene calling workflow | |
| 3 ============================== | |
| 4 | |
| 5 This Tool Shed Repository contains a workflow for the gene prediction of from a given nucleotide FASTA file. | |
| 6 | |
| 7 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. | |
| 8 | |
| 9 To run that worflow glimmer_ und the EMBOSS_ suite is required. Both can be installed from the Tool Shed. | |
| 10 | |
| 11 .. _glimmer: http://www.cbcb.umd.edu/software/glimmer/ | |
| 12 .. _EMBOSS: http://emboss.sourceforge.net/ | |
| 13 | |
| 14 | 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). | |
| 15 | |
| 16 EMBOSS: The European Molecular Biology Open Software Suite (2000) | |
| 17 Rice,P. Longden,I. and Bleasby,A. | |
| 18 Trends in Genetics 16, (6) pp276--277 | |
| 19 | |
| 20 ************ | |
| 21 Availability | |
| 22 ************ | |
| 23 | |
| 24 This workflow is available on the main Galaxy Tool Shed: | |
| 25 http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_gene_calling_workflow | |
| 26 | |
| 27 Development is being done here: | |
| 28 https://github.com/bgruening/galaxytools/workflows/glimmer3/ |