Annotation DatabasesΒΆ
Funannotate uses several publicly available databases, they can be installed with the funannotate setup
command. The currently installed databases and version numbers can be displayed with the funannotate database
command.
Initial setup is simple and requires only a path to a database location, this can (should) be set using the $FUNANNOTATE_DB environmental variable. If $FUNANNOTATE_DB is set, then the script will use that location by default, otherwise you will need to specify a location to the script i.e.:
funannotate setup -d $HOME/funannotate_db
You could then update the databases if $FUNANNOTATE_DB is set like this:
funannotate setup -i all --update
#or force update of just one database
funannotate setup -i uniprot --force
This will download and format the databases, they can be displayed like so:
$ funannotate database
Funannotate Databases currently installed:
Database Type Version Date Num_Records Md5checksum
pfam hmmer3 32.0 2018-08 17929 de7496fad69c1040fd74db1cb5eef0fc
gene2product text 1.45 2019-07-31 30103 657bb30cf3247fcb74ca4f51a4ab7c18
interpro xml 76.0 2019-09-18 37113 328f66a791f9866783764f24a74a5aa3
dbCAN hmmer3 8.0 2019-08-08 607 51c724c1f9ac45687f08d0faa689ed58
busco_outgroups outgroups 1.0 2019-10-20 7 6795b1d4545850a4226829c7ae8ef058
merops diamond 12.0 2017-10-04 5009 a6dd76907896708f3ca5335f58560356
mibig diamond 1.4 2019-10-20 31023 118f2c11edde36c81bdea030a0228492
uniprot diamond 2019_09 2019-10-16 561176 9fc7871b8c4e3b755fe2086d77ed0645
go text 2019-10-07 2019-10-07 47375 3bc9ba43a98bf8fcd01db6e7e7813dd2
repeats diamond 1.0 2019-10-20 11950 4e8cafc3eea47ec7ba505bb1e3465d21
To update a database type:
funannotate setup -i DBNAME -d $HOME/funannotate_db --force
To see install BUSCO outgroups type:
funannotate database --show-outgroups
To see BUSCO tree type:
funannotate database --show-buscos
Similarly, database sources can be updated with the funannotate setup
command, for example to update the gene2product database to its most recent version you would run:
$ funannotate setup -d $HOME/funannotate_db -i gene2product --update