Protein homology detection by HMM-HMM comparison

Protein homology detection by HMM–HMM comparison

Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and

Protein homology detection by HMM?CHMM comparison

MOTIVATION Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution. RESULTS We have generalized the alignment of protein sequences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile HMMs. We present a method for detecting distant homologous relationships between proteins based on t...

Identification of Divergent Protein Domains by Combining HMM-HMM Comparisons and Co-Occurrence Detection

Identification of protein domains is a key step for understanding protein function. Hidden Markov Models (HMMs) have proved to be a powerful tool for this task. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in sequenced organisms. This is done via sequence/HMM comparisons. However, this approach may lack sensitivity when searc...

Performance of an iterated T-HMM for homology detection

MOTIVATION Much information about new protein sequences is derived from identifying homologous proteins. Such tasks are difficult when the evolutionary relationships are distant. Some modern methods achieve better results by building a model of a set of related sequences, and then identifying new proteins that fit the model. A further advance was the development of iterative methods that refine...

Clause detection using HMM