Details
Description
Although hmmsearch does produce a 'result' when searching nucleotide using a DNA profile, the correct program to run is nhmmer. This is new in HMMER3.1 with the release note
"HMMER now includes tools that are specifically designed for DNA/DNA
comparison: nhmmer and nhmmscan. The most notable improvement over using HMMER3’s tools is the ability to search long (e.g. chromosome length) target sequences."
"HMMER now includes tools that are specifically designed for DNA/DNA
comparison: nhmmer and nhmmscan. The most notable improvement over using HMMER3’s tools is the ability to search long (e.g. chromosome length) target sequences."