Mercurial > repos > devteam > ncbi_blast_plus

annotate tool-data/blastdb_d.loc.sample @ 13:623f727cdff1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
author peterjc
date Fri, 14 Mar 2014 07:40:46 -0400
parents 9dabbfd73c8a
children c16c30e9ad5b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that is used to define a
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
2 #list of protein domain databases, using three columns tab separated
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
3 #(longer whitespace are TAB characters):
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
4 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
5 #<unique_id> <database_caption> <base_name_path>
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
6 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
7 #The captions typically contain spaces and might end with the build date.
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
8 #It is important that the actual database name does not have a space in it,
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
9 #and that there are only two tabs on each line.
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
10 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
11 #You can download the NCBI provided databases as tar-balls from here:
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
12 #ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
13 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
14 #So, for example, if your database is CDD and the path to your base name
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
15 #is /data/blastdb/Cdd, then the blastdb_d.loc entry would look like this:
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
16 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
17 #Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/Cdd
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
18 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
19 #and your /data/blastdb directory would contain all of the files associated
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
20 #with the database, /data/blastdb/Cdd.*.
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
21 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
22 #Your blastdb_d.loc file should include an entry per line for each "base name"
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
23 #you have stored. For example:
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
24 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
25 #Cdd NCBI CDD /data/blastdb/domains/Cdd
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
26 #Kog KOG (eukaryotes) /data/blastdb/domains/Kog
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
27 #Cog COG (prokaryotes) /data/blastdb/domains/Cog
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
28 #Pfam Pfam-A /data/blastdb/domains/Pfam
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
29 #Smart SMART /data/blastdb/domains/Smart
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
30 #Tigr TIGR /data/blastdb/domains/Tigr
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
31 #Prk Protein Clusters database /data/blastdb/domains/Prk
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
32 #...etc...
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
33 #
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
34 #See also blastdb.loc which is for any nucleotide BLAST database, and
9dabbfd73c8a Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
parents:
diff changeset
35 #blastdb_p.loc which is for any protein BLAST databases.