SALT (Sensitive and Accurate protein domain cLassification Tool) can accurately and sensitivity classify short reads of NGS into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families.
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Bioinformatics. 2013 Sep 1;29(17):2103-11. doi: 10.1093/bioinformatics/btt357. Epub 2013 Jun 19.
A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads.
Zhang Y1, Sun Y, Cole JR.