genewisedb - search modes

-protein

[default] single protein. Protein is a single protein sequence in fasta format

-prodb

protein fasta format db. Protein is a database of protein sequences in fasta format

-pfam

pfam hmm library. Protein is a database of HMMer2 models as a single file

-pfam2

pfam old style model directory (2.1). Protein is a directory of HMMs with a file called HMMs in it indicating which HMMs there. This is how Pfam databases 2.1 and lower were distributed

-hmmer

single hmmer HMM (version 2 compatible). Protein is a single HMM

-dnadb

[default] dna fasta database. The DNA sequence is a fasta format file with multiple sequences

-dnas

a single dna fasta sequence. The DNA sequence is a single sequence in fasta format