Mercurial > repos > bgruening > find_genes_located_nearby_workflow
changeset 0:db68266f7364 draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 24 Feb 2015 04:48:44 -0500 |
| parents | |
| children | d734579c3307 |
| files | WP_037658548.fasta WP_037658557.fasta find_genes_located_nearby.ga find_genes_located_nearby.png readme.md repository_dependencies.xml |
| diffstat | 6 files changed, 649 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WP_037658548.fasta Tue Feb 24 04:48:44 2015 -0500 @@ -0,0 +1,9 @@ +>gi|739806613|ref|WP_037658548.1| beta-ACP synthase [Streptomyces aurantiacus] +MSGRRVVVTGMEVLAPGGVGTDNFWSLLSEGRTATRGITFFDPAQFRSRVAAEIDFDPYAHGLTPQEVRR +MDRAAQFAVVAARGAVADSGLDTDTLDPYRIGVTIGSAVGATMSLDEDYRVVSDAGRLDLVDHTYADPFF +YNYFVPSSFATEVARLVGAQGPSSVVSAGCTSGLDSVGYAVELIREGTADVMVAGATDAPISPITMACFD +AIKATTPRHDDPEHASRPFDDTRNGFVLGEGTAVFVLEELESARRRGARIYAEIAGYATRSNAYHMTGLR +PDGAEMAEAITVALDEARMNPTAIDYINAHGSGTKQNDRHETAAFKRSLGEHAYRTPVSSIKSMVGHSLG +AIGSIEIAASILAIQHDVVPPTANLHTPDPQCDLDYVPLNAREQIVDAVLTVGSGFGGFQSAMVLAQPER +NAA +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WP_037658557.fasta Tue Feb 24 04:48:44 2015 -0500 @@ -0,0 +1,7 @@ +>gi|739806622|ref|WP_037658557.1| cytochrome P450 [Streptomyces aurantiacus] +MQRTCPFSVPPVYTKFREESPITQVVLPDGGKAWLVTKYDDVRAVMANPKLSSDRRAPDFPVVVPGQNAA +LAKHAPFMIILDGAEHAAARRPVISEFSVRRVAAMKPRIQEIVDGFIDDMLKMPKPVDLNQVFSLPVPSL +VVSEILGMPYEGHEYFMELAEILLRRTTDEQGRIAVSVELRKYMDKLVEEKIENPGDDLLSRQIELQRQQ +GGIDRPQLASLCLLVLLAGHETTANMINLGVFSMLTKPELLAEIKADPSKTPKAVDELLRFYTIPDFGAH +RLALDDVEIGGVLIRKGEAVIASTFAANRDPAVFDDPEELDFGRDARHHVAFGYGPHQCLGQNLGRLELQ +VVFDTLFRRLPELRLAVPEEELSFKSDALVYGLYELPVTW
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Tue Feb 24 04:48:44 2015 -0500 @@ -0,0 +1,84 @@ +Galaxy workflow for the identification of candidate genes clusters +------------------------------------------------------------------ + +This approach screens two proteins against all nucleotide sequence from the +NCBI nt database within hours on our cluster, leading to all organisms with an inter- +esting gene structure for further investigation. As usual in Galaxy workflows every +parameter, including the proximity distance, can be changed and additional steps +can be easily added. For example additional filtering to refine the initial BLAST +hits, or inclusion of a third query sequence. + + + + +Sample Data +=========== + +As an example, we will use two protein sequences from *Streptomyces aurantiacus* +that are part of a gene cluster, responsible for metabolite producion. + +You can upload both sequences directly into Galaxy using the "Upload File" tool +with either of these URLs - Galaxy should recognise this is FASTA files. + + * https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/WP_037658548.fasta + * https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/WP_037658557.fasta + +In addition you can find both sequences at the NCBI server: + * http://www.ncbi.nlm.nih.gov/protein/739806622 (cytochrome P450) + +```text +>gi|739806622|ref|WP_037658557.1| cytochrome P450 [Streptomyces aurantiacus] +MQRTCPFSVPPVYTKFREESPITQVVLPDGGKAWLVTKYDDVRAVMANPKLSSDRRAPDFPVVVPGQNAA +LAKHAPFMIILDGAEHAAARRPVISEFSVRRVAAMKPRIQEIVDGFIDDMLKMPKPVDLNQVFSLPVPSL +VVSEILGMPYEGHEYFMELAEILLRRTTDEQGRIAVSVELRKYMDKLVEEKIENPGDDLLSRQIELQRQQ +GGIDRPQLASLCLLVLLAGHETTANMINLGVFSMLTKPELLAEIKADPSKTPKAVDELLRFYTIPDFGAH +RLALDDVEIGGVLIRKGEAVIASTFAANRDPAVFDDPEELDFGRDARHHVAFGYGPHQCLGQNLGRLELQ +VVFDTLFRRLPELRLAVPEEELSFKSDALVYGLYELPVTW +``` + + * http://www.ncbi.nlm.nih.gov/protein/739806613 (beta-ACP synthase) + +``` +>gi|739806613|ref|WP_037658548.1| beta-ACP synthase [Streptomyces aurantiacus] +MSGRRVVVTGMEVLAPGGVGTDNFWSLLSEGRTATRGITFFDPAQFRSRVAAEIDFDPYAHGLTPQEVRR +MDRAAQFAVVAARGAVADSGLDTDTLDPYRIGVTIGSAVGATMSLDEDYRVVSDAGRLDLVDHTYADPFF +YNYFVPSSFATEVARLVGAQGPSSVVSAGCTSGLDSVGYAVELIREGTADVMVAGATDAPISPITMACFD +AIKATTPRHDDPEHASRPFDDTRNGFVLGEGTAVFVLEELESARRRGARIYAEIAGYATRSNAYHMTGLR +PDGAEMAEAITVALDEARMNPTAIDYINAHGSGTKQNDRHETAAFKRSLGEHAYRTPVSSIKSMVGHSLG +AIGSIEIAASILAIQHDVVPPTANLHTPDPQCDLDYVPLNAREQIVDAVLTVGSGFGGFQSAMVLAQPER +NAA +``` + + +Citation +======== + +If you use this workflow directly, or a derivative of it, or the associated +NCBI BLAST wrappers for Galaxy, in work leading to a scientific publication, +please cite: + +Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo +NCBI BLAST+ integrated into Galaxy + +http://biorxiv.org/content/early/2015/01/21/014043 +http://dx.doi.org/10.1101/014043 + + +Availability +============ + +This workflow is available on the main Galaxy Tool Shed: + +http://toolshed.g2.bx.psu.edu/view/bgruening/find_genes_located_nearby_workflow + +Development is being done on github: + +https://github.com/bgruening/galaxytools/workflows/ncbi_blast_plus/ + + +Dependencies +============ + +These dependencies should be resolved automatically via the Galaxy Tool Shed: + +* http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue Feb 24 04:48:44 2015 -0500 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="This workflow requires the NCBI BLAST tools."> + <repository changeset_revision="2fe07f50a41e" name="ncbi_blast_plus" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories>