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Galaxy workflow for the identification of candidate genes clusters
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This approach screens three proteins against a given genome sequence, leading to a genome position
were all three genes are located nearby. 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.

.. image:: https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby/find_three_genes_located_nearby.png


Sample Data
===========

As an example, we will use three protein sequences from *Pan troglodytes* (Chimpanzee)
which are part of the β-globin cluster.

You can upload all sequences directly into Galaxy using the "Upload tool"
with either of these URLs - Galaxy should recognise this is FASTA files.

Query sequences:

* `P61920.fasta <https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby/P61920.fasta>`_
* `P61921.fasta <https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby/P61921.fasta>`_
* `Q6LDH1.fasta <https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby/Q6LDH1.fasta>`_

Genome sequence:

* http://hgdownload.cse.ucsc.edu/goldenPath/rn6/bigZips/rn6.fa.gz


In addition you can find the query sequences at the UniProt server:
 * http://www.uniprot.org/uniprot/P61920 (Hemoglobin subunit gamma-1)
   ::

     >sp|P61920|HBG1_PANTR Hemoglobin subunit gamma-1 OS=Pan troglodytes GN=HBG1 PE=1 SV=2
     MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK
     VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG
     KEFTPEVQASWQKMVTAVASALSSRYH


 * http://www.uniprot.org/uniprot/P61921 (Hemoglobin subunit gamma-2)
   ::

     >sp|P61921|HBG2_PANTR Hemoglobin subunit gamma-2 OS=Pan troglodytes GN=HBG2 PE=1 SV=2
     MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK
     VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG
     KEFTPEVQASWQKMVTGVASALSSRYH


 * http://www.uniprot.org/uniprot/Q6LDH1 (Hemoglobin subunit epsilon)
   ::

     >sp|Q6LDH1|HBE_PANTR Hemoglobin subunit epsilon OS=Pan troglodytes GN=HBE1 PE=2 SV=3
     MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPK
     VKAHGKKVLTSFGDAIKNMDNLKPAFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFG
     KEFTPEVQAAWQKLVSAVAIALAHKYH


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_three_genes_located_nearby_workflow

Development is being done on github:

https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby


Dependencies
============

These dependencies should be resolved automatically via the Galaxy Tool Shed:

* http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus