Mercurial > repos > bgruening > find_three_genes_located_nearby_workflow
changeset 0:e42f2c5118ac draft
Imported from capsule None
| author | bgruening |
|---|---|
| date | Tue, 17 Mar 2015 09:40:46 -0400 |
| parents | |
| children | 12a1efdaeb5b |
| files | P61920.fasta P61921.fasta Q6LDH1.fasta find_three_genes_located_nearby.ga find_three_genes_located_nearby.png readme.rst repository_dependencies.xml |
| diffstat | 7 files changed, 1071 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/P61920.fasta Tue Mar 17 09:40:46 2015 -0400 @@ -0,0 +1,4 @@ +>sp|P61920|HBG1_PANTR Hemoglobin subunit gamma-1 OS=Pan troglodytes GN=HBG1 PE=1 SV=2 +MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK +VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG +KEFTPEVQASWQKMVTAVASALSSRYH
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/P61921.fasta Tue Mar 17 09:40:46 2015 -0400 @@ -0,0 +1,4 @@ +>sp|P61921|HBG2_PANTR Hemoglobin subunit gamma-2 OS=Pan troglodytes GN=HBG2 PE=1 SV=2 +MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK +VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG +KEFTPEVQASWQKMVTGVASALSSRYH
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Q6LDH1.fasta Tue Mar 17 09:40:46 2015 -0400 @@ -0,0 +1,4 @@ +>sp|Q6LDH1|HBE_PANTR Hemoglobin subunit epsilon OS=Pan troglodytes GN=HBE1 PE=2 SV=3 +MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPK +VKAHGKKVLTSFGDAIKNMDNLKPAFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFG +KEFTPEVQAAWQKLVSAVAIALAHKYH
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Tue Mar 17 09:40:46 2015 -0400 @@ -0,0 +1,90 @@ +Galaxy workflow for the identification of candidate genes clusters +------------------------------------------------------------------ + +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 + + +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue Mar 17 09:40:46 2015 -0400 @@ -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>