Mercurial > repos > devteam > ncbi_blast_plus
comparison tool-data/blastdb_d.loc.sample @ 9:9dabbfd73c8a draft
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
Also includes other minor improvements.
| author | peterjc |
|---|---|
| date | Thu, 25 Apr 2013 09:38:37 -0400 |
| parents | |
| children | c16c30e9ad5b |
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| 8:1f546099212f | 9:9dabbfd73c8a |
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| 1 #This is a sample file distributed with Galaxy that is used to define a | |
| 2 #list of protein domain databases, using three columns tab separated | |
| 3 #(longer whitespace are TAB characters): | |
| 4 # | |
| 5 #<unique_id> <database_caption> <base_name_path> | |
| 6 # | |
| 7 #The captions typically contain spaces and might end with the build date. | |
| 8 #It is important that the actual database name does not have a space in it, | |
| 9 #and that there are only two tabs on each line. | |
| 10 # | |
| 11 #You can download the NCBI provided databases as tar-balls from here: | |
| 12 #ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ | |
| 13 # | |
| 14 #So, for example, if your database is CDD and the path to your base name | |
| 15 #is /data/blastdb/Cdd, then the blastdb_d.loc entry would look like this: | |
| 16 # | |
| 17 #Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/Cdd | |
| 18 # | |
| 19 #and your /data/blastdb directory would contain all of the files associated | |
| 20 #with the database, /data/blastdb/Cdd.*. | |
| 21 # | |
| 22 #Your blastdb_d.loc file should include an entry per line for each "base name" | |
| 23 #you have stored. For example: | |
| 24 # | |
| 25 #Cdd NCBI CDD /data/blastdb/domains/Cdd | |
| 26 #Kog KOG (eukaryotes) /data/blastdb/domains/Kog | |
| 27 #Cog COG (prokaryotes) /data/blastdb/domains/Cog | |
| 28 #Pfam Pfam-A /data/blastdb/domains/Pfam | |
| 29 #Smart SMART /data/blastdb/domains/Smart | |
| 30 #Tigr TIGR /data/blastdb/domains/Tigr | |
| 31 #Prk Protein Clusters database /data/blastdb/domains/Prk | |
| 32 #...etc... | |
| 33 # | |
| 34 #See also blastdb.loc which is for any nucleotide BLAST database, and | |
| 35 #blastdb_p.loc which is for any protein BLAST databases. |