# HG changeset patch # User bgruening # Date 1426599646 14400 # Node ID e42f2c5118aced4c4a9bd1c4fd67e2011bf97738 Imported from capsule None diff -r 000000000000 -r e42f2c5118ac P61920.fasta --- /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 diff -r 000000000000 -r e42f2c5118ac P61921.fasta --- /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 diff -r 000000000000 -r e42f2c5118ac Q6LDH1.fasta --- /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 diff -r 000000000000 -r e42f2c5118ac find_three_genes_located_nearby.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/find_three_genes_located_nearby.ga Tue Mar 17 09:40:46 2015 -0400 @@ -0,0 +1,965 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Input are two protein genes in FASTA format. 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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 `_ +* `P61921.fasta `_ +* `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 diff -r 000000000000 -r e42f2c5118ac repository_dependencies.xml --- /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 @@ + + + +