GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
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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.
This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used.
Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss.