Hi All, I was trying to develop an algorithm for describing/predicting a pattern (e.g. transmembrane region, signal peptide etc) in protein sequences. I want to derive this pattern from the multiple sequence alignments. But I was wondering if I should use substitution matrices or HMMs to describe/represent these patterns. Are there any definite advantages of using one over the other ? Does the choice depend on what I am trying to define ? Can somebody please direct me to relevant literature or suggest something from personal experience ? Thanks in advance, Manisha Goel -------------- next part -------------- An HTML attachment was scrubbed... URL: http://bioinformatics.org/pipermail/ssml-general/attachments/20041029/2cd3064e/attachment.htm