GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
...It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed.
Basically, GenSeed-HMM performs three operations, repeatedly:
- recruit reads by matching them to a seed
- assemble the recruited reads (including previously assembled contigs)
- generate new seeds (for the next round of progressive assembly) from the extremities of all generated contigs
The first seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity.
...