Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'

Background: Many proposed statistical measures can efficiently compare protein sequence to further infer protein structure, function and evolutionary information. They share the same idea of using k-word frequencies of protein sequences. Given a protein sequence, the information on its related protein sequences hasn't been used for protein sequence comparison until now. This paper proposed a scheme to construct protein 'sequence space' which was associated with protein sequences related to the given protein, and the performances of statistical measures were compared when they explored the information on protein 'sequence space' or not. This paper also presented two statistical measures for protein: gre.k (generalized relative entropy) and gsm.k (gapped similarity measure). Results: We tested statistical measures based on protein 'sequence space' or not with three data sets. This not only offers the systematic and quantitative experimental assessment ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Qi Dai, Tian-Ming Wang
• Keywords: BMCBI 2008, Protein, Protein Sequences, Statistical Measure