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placeholder repo for issues migrating from JIRA system, to be moved to their appropriate places later
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Create gene family blast targets at PeanutBase and LegumeInfo #206

Closed adf-ncgr closed 9 years ago

adf-ncgr commented 9 years ago

Add gene family consensus sequences as (peptide) blast targets at PeanutBase and LegumeInfo. Hits ought to link to the corresponding families, e.g. http://legumeinfo.org/chado_phylotree/phytozome_10.54635005

[LEGUME-238] created by scannon

adf-ncgr commented 9 years ago

I have generated blast targets for the phytozome 10 gene families. These are at
/usr/local/www/drupal7/files/BLAST
for both lis-stage and peanutbase-stage . The blast target name is "gene_family_consensus"

Next steps: configure the blast module to include this blast target for blastp and blastx at both web sites, with link-outs to e.g. http://legumeinfo.org/chado_phylotree/phytozome_10.54635005

by scannon

adf-ncgr commented 9 years ago

Blast target generation is documented here:
/usr/local/www/drupal7/files/BLAST/format_gene_fam_targets.sh

In particular, the gene family consensus sequences are on cicer at
PATH_TO_GENEFAMS=/data/genefams/trees_public2.used_for_loading

and the makeblastdb command is
ls $PATH_TO_GENEFAMS/03_consensus | xargs -I{} cat $PATH_TO_GENEFAMS/03_consensus/{} | sed 's/-consensus//' \

makeblastdb -in - -dbtype prot -out gene_family_consensus -title gene_family_consensus -hash_index

by scannon

adf-ncgr commented 9 years ago

I configured the BLAST with the new target and provided the link out functionality in both lis-stage and peanubase-stage. I updated the .pal targets to include the newly added protein sequence. The new target was names as "Gene Family Sequence".

by deepakbvs