Mercurial > repos > bgruening > find_genes_located_nearby_workflow

diff readme.md @ 0:db68266f7364 draft
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author: bgruening
date: Tue, 24 Feb 2015 04:48:44 -0500
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+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.
+
+![Workflow Image](https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/find_genes_located_nearby.png)
+
+
+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
author	bgruening
date	Tue, 24 Feb 2015 04:48:44 -0500
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