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1 This package is a Galaxy workflow for gene prediction using Glimmer3.
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2
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3 It uses the Glimmer3 tool (Delcher et al. 2007) trained on a known set of
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4 genes to generate gene predictions on a new genome, and then calls EMBOSS
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5 (Rice et al. 2000) to translate the predictions into a FASTA file of
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6 predicted protein sequences. The workflow requires two input files:
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7
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8 * Nucleotide FASTA file of know gene sequences (training set)
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9 * Nucleotide FASTA file of genome sequence or assembled contigs
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10
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11 First an interpolated context model (ICM) is built from the set of known
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12 genes, preferably from the closest relative organism(s) available. Next this
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13 ICM model is used to predict genes on the genomic FASTA file. This produces
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14 a FASTA file of the predicted gene nucleotide sequences, which is translated
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15 into protein sequences using the EMBOSS tool transeq.
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16
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17 Glimmer is intended for finding genes in microbial DNA, especially bacteria,
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18 archaea, and viruses.
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19
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20 See http://www.galaxyproject.org for information about the Galaxy Project.
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21
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22
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23 Sample Data
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24 ===========
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25
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26 As an example, we will use the first public assembly of the 2011 Shiga-toxin
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27 producing *Escherichia coli* O104:H4 outbreak in Germany. This was part of the
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28 open-source crowd-sourcing analysis described in Rohde et al. (2011) and here:
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29 https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki
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30
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31 You can upload this assembly directly into Galaxy using the "Upload File" tool
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32 with either of these URLs - Galaxy should recognise this is a FASTA file with
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33 3,057 sequences:
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34
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35 * http://static.xbase.ac.uk/files/results/nick/TY2482/TY2482.fasta.txt
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36 * https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/blob/master/strains/TY2482/seqProject/BGI/assemblies/NickLoman/TY2482.fasta.txt
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37
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38 This FASTA file ``TY2482.fasta.txt`` was the initial TY-2482 strain assembled
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39 by Nick Loman from 5 runs of Ion Torrent data released by the BGI, using the
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40 MIRA 3.2 assembler. It was initially released via his blog,
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41 http://pathogenomics.bham.ac.uk/blog/2011/06/ehec-genome-assembly/
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42
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43 We will also need a training set of known *E. coli* genes, for example the
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44 model strain *Escherichia coli* str. K-12 substr. MG1655 which is well
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45 annotated. You can upload the NCBI FASTA file ``NC_000913.ffn`` of the
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46 gene nucleotide sequences directly into Galaxy via this URL, which Galaxy
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47 should recognise as a FASTA file with 4,321 sequences:
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48
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49 * ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/NC_000913.ffn
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50
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51 Then run the workflow, which should produce 2,333 predicted genes for the
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52 TY2482 assembly (two FASTA files, nucleotide and protein sequences).
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53
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54
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55 Citation
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56 ========
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57
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58 If you use this workflow directly, or a derivative of it, or the associated
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59 Glimmer wrappers for Galaxy, in work leading to a scientific publication,
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60 please cite:
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61
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62 Cock, P.J.A., Grüning, B., Paszkiewicz, K. and Pritchard, L. (2013)
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63 Galaxy tools and workflows for sequence analysis with applications in
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64 molecular plant pathology. (Submitted).
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65
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66 For Glimmer3 please cite:
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67
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68 Delcher, A.L., Bratke, K.A., Powers, E.C., and Salzberg, S.L. (2007)
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69 Identifying bacterial genes and endosymbiont DNA with Glimmer.
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70 Bioinformatics 23(6), 673-679.
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71 http://dx.doi.org/10.1093/bioinformatics/btm009
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72
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73 For EMBOSS please cite:
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74
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75 Rice, P., Longden, I. and Bleasby, A. (2000)
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76 EMBOSS: The European Molecular Biology Open Software Suite
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77 Trends in Genetics 16(6), 276-277.
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78 http://dx.doi.org/10.1016/S0168-9525(00)02024-2
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79
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80
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81 Additional References
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82 =====================
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83
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84 Rohde, H., Qin, J., Cui, Y., Li, D., Loman, N.J., et al. (2011)
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85 Open-source genomic analysis of shiga-toxin-producing E. coli O104:H4.
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86 New England Journal of Medicine 365, 718-724.
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87 http://dx.doi.org/10.1056/NEJMoa1107643
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88
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89
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90 Availability
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91 ============
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92
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93 This workflow is available on the main Galaxy Tool Shed:
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94
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95 http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_gene_calling_workflow
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96
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97 Development is being done on github:
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98
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99 https://github.com/bgruening/galaxytools/workflows/glimmer3/
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100
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101
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102 Dependencies
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103 ============
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104
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105 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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106
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107 * http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer3
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108 * http://toolshed.g2.bx.psu.edu/view/devteam/emboss_5
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