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1 Galaxy wrapper for RepeatMasker
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2 =====================================
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3
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4 This wrapper is copyright 2012 by Björn Grüning.
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5
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6 This is a wrapper for the command line tool of GlimmerHMM.
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7 http://www.cbcb.umd.edu/software/GlimmerHMM/
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8
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9 GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM,
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10 additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes
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11 Interpolated Markov Models for the coding and noncoding models.
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12 Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).
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13
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14 Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2878-2879.
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15 Pertea, M. and S. L. Salzberg (2002). "Computational gene finding in plants." Plant Molecular Biology 48(1-2): 39-48.
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16 The Arabidopsis Genome Initiative, (2000) "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana", Nature. Dec 14; 408(6814):796-815.
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17 Pertea, M., S. L. Salzberg, et al. (2000). "Finding genes in Plasmodium falciparum." Nature 404(6773): 34; discussion 34-5.
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18 Salzberg, S. L., M. Pertea, et al. (1999). "Interpolated Markov models for eukaryotic gene finding." Genomics 59(1): 24-31.
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19
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20
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21 Installation
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22 ============
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23
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24 To install Glimmer3, please download GlimmerHMM from
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25
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26 ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/
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27
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28 and follow the installation instructions.
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29 To extract the glimmerHMM predicted genes, the GFF Parser from Brad Chapman (ttp://github.com/chapmanb/bcbb/tree/master/gff) was used and is included.
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30
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31 To install the wrapper copy the glimmerHMM folder in the galaxy tools
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32 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
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33 For example:
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34
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35 <tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_predict.xml" />
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36 <tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_to_sequence.xml" />
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37
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38
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39 History
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40 =======
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41
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42 v0.1 - Initial public release
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43
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44
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45 Wrapper Licence (MIT/BSD style)
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46 ===============================
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47
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48 Permission to use, copy, modify, and distribute this software and its
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49 documentation with or without modifications and for any purpose and
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50 without fee is hereby granted, provided that any copyright notices
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51 appear in all copies and that both those copyright notices and this
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52 permission notice appear in supporting documentation, and that the
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53 names of the contributors or copyright holders not be used in
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54 advertising or publicity pertaining to distribution of the software
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55 without specific prior permission.
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56
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57 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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58 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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59 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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60 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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61 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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62 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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63 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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64 OR PERFORMANCE OF THIS SOFTWARE.
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65
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