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diff --git a/academic/HMMER/README b/academic/HMMER/README new file mode 100644 index 0000000000..7129424d65 --- /dev/null +++ b/academic/HMMER/README @@ -0,0 +1,19 @@ +HMMER: biosequence analysis using profile hidden Markov models + +HMMER is used for searching sequence databases for sequence homologs, +and for making sequence alignments. It implements methods using +probabilistic models called profile hidden Markov models (profile HMMs). + +HMMER is often used together with a profile database, such as Pfam or +many of the databases that participate in Interpro. But HMMER can also +work with query sequences, not just profiles, just like BLAST. For +example, you can search a protein query sequence against a database with +phmmer, or do an iterative search with jackhmmer. + +HMMER is designed to detect remote homologs as sensitively as possible, +relying on the strength of its underlying probability models. In the +past, this strength came at significant computational expense, but as +of the new HMMER3 project, HMMER is now essentially as fast as BLAST. + +Publications: +http://hmmer.org/publications.html |