Mercurial > repos > konradpaszkiewicz > interproscan
annotate README_INTERPROSCAN @ 0:49e20fa2c66d
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | konradpaszkiewicz |
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date | Tue, 07 Jun 2011 17:27:16 -0400 |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #Created 07/01/2011 - Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter |
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49e20fa2c66d
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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3 The attached is a crude wrapper script for Interproscan. Typically this is useful when one wants to produce an annotation which is not based on sequence |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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4 similarity. E.g after a denovo transcriptome assembly, each transcript could be translated and run through this tool. |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 Prerequisites: |
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7 |
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8 1. A working installation of Interproscan on your Galaxy server/cluster. |
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10 Limitations: |
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11 |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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12 Currently it is setup to work with PFAM only due to the heavy computational demands Interproscan makes. |
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13 |
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14 Input formats: |
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49e20fa2c66d
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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16 The standard interproscan input is either genomic or protein sequences. In the case of genomic sequences Interproscan will of run an ORF |
49e20fa2c66d
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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17 prediction tool. However this tends to lose the ORF information (e.g. start/end co-ordinates) from the header. As such the requirement here is to input ORF |
49e20fa2c66d
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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18 sequences (e.g. from EMBOSS getorf) and to then replace any spaces in the FASTA header with underscores. This workaround generally preserves the relevant |
49e20fa2c66d
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
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19 positional information. |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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