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1 Galaxy workflow for the identification of candidate genes clusters
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2 ------------------------------------------------------------------
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3
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4 This approach screens three proteins against a given genome sequence, leading to a genome position
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5 were all three genes are located nearby. As usual in Galaxy workflows every
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6 parameter, including the proximity distance, can be changed and additional steps
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7 can be easily added. For example additional filtering to refine the initial BLAST
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8 hits, or inclusion of a third query sequence.
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9
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10 .. image:: https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby/find_three_genes_located_nearby.png
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11
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12
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13 Sample Data
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14 ===========
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15
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16 As an example, we will use three protein sequences from *Pan troglodytes* (Chimpanzee)
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17 which are part of the β-globin cluster.
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18
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19 You can upload all sequences directly into Galaxy using the "Upload tool"
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20 with either of these URLs - Galaxy should recognise this is FASTA files.
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21
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22 Query sequences:
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23
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24 * `P61920.fasta <https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby/P61920.fasta>`_
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25 * `P61921.fasta <https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby/P61921.fasta>`_
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26 * `Q6LDH1.fasta <https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby/Q6LDH1.fasta>`_
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27
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28 Genome sequence:
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29
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30 * http://hgdownload.cse.ucsc.edu/goldenPath/rn6/bigZips/rn6.fa.gz
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31
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32
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33 In addition you can find the query sequences at the UniProt server:
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34 * http://www.uniprot.org/uniprot/P61920 (Hemoglobin subunit gamma-1)
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35 ::
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36
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37 >sp|P61920|HBG1_PANTR Hemoglobin subunit gamma-1 OS=Pan troglodytes GN=HBG1 PE=1 SV=2
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38 MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK
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39 VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG
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40 KEFTPEVQASWQKMVTAVASALSSRYH
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41
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42
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43 * http://www.uniprot.org/uniprot/P61921 (Hemoglobin subunit gamma-2)
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44 ::
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45
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46 >sp|P61921|HBG2_PANTR Hemoglobin subunit gamma-2 OS=Pan troglodytes GN=HBG2 PE=1 SV=2
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47 MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK
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48 VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG
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49 KEFTPEVQASWQKMVTGVASALSSRYH
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50
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51
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52 * http://www.uniprot.org/uniprot/Q6LDH1 (Hemoglobin subunit epsilon)
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53 ::
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54
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55 >sp|Q6LDH1|HBE_PANTR Hemoglobin subunit epsilon OS=Pan troglodytes GN=HBE1 PE=2 SV=3
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56 MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPK
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57 VKAHGKKVLTSFGDAIKNMDNLKPAFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFG
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58 KEFTPEVQAAWQKLVSAVAIALAHKYH
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59
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60
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61 Citation
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62 ========
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63
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64 If you use this workflow directly, or a derivative of it, or the associated
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65 NCBI BLAST wrappers for Galaxy, in work leading to a scientific publication,
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66 please cite:
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67
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68 Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo
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69 NCBI BLAST+ integrated into Galaxy
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70
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71 * http://biorxiv.org/content/early/2015/01/21/014043
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72 * http://dx.doi.org/10.1101/014043
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73
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74
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75 Availability
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76 ============
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77
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78 This workflow is available on the main Galaxy Tool Shed:
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79
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80 http://toolshed.g2.bx.psu.edu/view/bgruening/find_three_genes_located_nearby_workflow
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81
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82 Development is being done on github:
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83
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84 https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby
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85
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86
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87 Dependencies
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88 ============
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89
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90 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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91
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92 * http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
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