About the Databases

dammit uses the following databases:

1. Pfam-A

   Pfam-A is a collection of protein domain profiles for use with profile hidden markov model programs like hmmer. These searches are moderately fast and very sensitive, and the Pfam database is very well curated. Pfam is used during TransDecoder's ORF finding and for annotation assignment.

2. Rfam

   Rfam is a collection of RNA covariance models for use with programs like Infernal. Covariance models describe RNA secondary structure, and Rfam is a curated database of non-coding RNAs.

3. OrthoDB

   OrthoDB is a curated database of orthologous genes. It attempts to classify proteins from all major groups of eukaryotes and trace them back to their ancestral ortholog.

4. BUSCO

   BUSCO databases are collections of "core" genes for major domains of life. They are used with an accompanying BUSCO program which assesses the completeness of a genome, transcriptome, or list of genes. There are multiple BUSCO databases, and which one you use depends on your particular organism. Currently available databases are:

   1. Metazoa
   2. Vertebrata
   3. Arthropoda
   4. Eukaryota

   dammit uses the metazoa database by default, but different databases can be used with the --busco-group parameter. You should try to use the database which most closely bounds your organism.

5. uniref90

   uniref is a curated collection of most known proteins, clustered at a 90% similarity threshold. This database is comprehensive, and thus quite enormous. dammit does not include it by default due to its size, but it can be installed and used with the --full flag.

A command using all of these potential options and databases might look like:

dammit databases --install --database-dir /path/to/dbs --full --busco-group arthropoda