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