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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 two proteins against all nucleotide sequence from the
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5 NCBI nt database within hours on our cluster, leading to all organisms with an inter-
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6 esting gene structure for further investigation. As usual in Galaxy workflows every
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7 parameter, including the proximity distance, can be changed and additional steps
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8 can be easily added. For example additional filtering to refine the initial BLAST
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9 hits, or inclusion of a third query sequence.
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10
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11 
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12
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13
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14 Sample Data
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15 ===========
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16
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17 As an example, we will use two protein sequences from *Streptomyces aurantiacus*
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18 that are part of a gene cluster, responsible for metabolite producion.
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19
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20 You can upload both sequences directly into Galaxy using the "Upload File" tool
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21 with either of these URLs - Galaxy should recognise this is FASTA files.
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22
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23 * https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/WP_037658548.fasta
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24 * https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/WP_037658557.fasta
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25
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26 In addition you can find both sequences at the NCBI server:
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27 * http://www.ncbi.nlm.nih.gov/protein/739806622 (cytochrome P450)
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28
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29 ```text
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30 >gi|739806622|ref|WP_037658557.1| cytochrome P450 [Streptomyces aurantiacus]
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31 MQRTCPFSVPPVYTKFREESPITQVVLPDGGKAWLVTKYDDVRAVMANPKLSSDRRAPDFPVVVPGQNAA
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32 LAKHAPFMIILDGAEHAAARRPVISEFSVRRVAAMKPRIQEIVDGFIDDMLKMPKPVDLNQVFSLPVPSL
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33 VVSEILGMPYEGHEYFMELAEILLRRTTDEQGRIAVSVELRKYMDKLVEEKIENPGDDLLSRQIELQRQQ
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34 GGIDRPQLASLCLLVLLAGHETTANMINLGVFSMLTKPELLAEIKADPSKTPKAVDELLRFYTIPDFGAH
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35 RLALDDVEIGGVLIRKGEAVIASTFAANRDPAVFDDPEELDFGRDARHHVAFGYGPHQCLGQNLGRLELQ
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36 VVFDTLFRRLPELRLAVPEEELSFKSDALVYGLYELPVTW
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37 ```
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38
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39 * http://www.ncbi.nlm.nih.gov/protein/739806613 (beta-ACP synthase)
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40
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41 ```
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42 >gi|739806613|ref|WP_037658548.1| beta-ACP synthase [Streptomyces aurantiacus]
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43 MSGRRVVVTGMEVLAPGGVGTDNFWSLLSEGRTATRGITFFDPAQFRSRVAAEIDFDPYAHGLTPQEVRR
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44 MDRAAQFAVVAARGAVADSGLDTDTLDPYRIGVTIGSAVGATMSLDEDYRVVSDAGRLDLVDHTYADPFF
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45 YNYFVPSSFATEVARLVGAQGPSSVVSAGCTSGLDSVGYAVELIREGTADVMVAGATDAPISPITMACFD
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46 AIKATTPRHDDPEHASRPFDDTRNGFVLGEGTAVFVLEELESARRRGARIYAEIAGYATRSNAYHMTGLR
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47 PDGAEMAEAITVALDEARMNPTAIDYINAHGSGTKQNDRHETAAFKRSLGEHAYRTPVSSIKSMVGHSLG
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48 AIGSIEIAASILAIQHDVVPPTANLHTPDPQCDLDYVPLNAREQIVDAVLTVGSGFGGFQSAMVLAQPER
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49 NAA
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50 ```
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51
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52
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53 Citation
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54 ========
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55
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56 If you use this workflow directly, or a derivative of it, or the associated
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57 NCBI BLAST wrappers for Galaxy, in work leading to a scientific publication,
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58 please cite:
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59
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60 Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo
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61 NCBI BLAST+ integrated into Galaxy
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62
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63 http://biorxiv.org/content/early/2015/01/21/014043
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64 http://dx.doi.org/10.1101/014043
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65
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66
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67 Availability
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68 ============
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69
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70 This workflow is available on the main Galaxy Tool Shed:
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71
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72 http://toolshed.g2.bx.psu.edu/view/bgruening/find_genes_located_nearby_workflow
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73
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74 Development is being done on github:
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75
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76 https://github.com/bgruening/galaxytools/workflows/ncbi_blast_plus/
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77
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78
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79 Dependencies
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80 ============
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81
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82 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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83
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84 * http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
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