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