• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.7-11
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• 2007

Methods for making scoring matrix based on phylogenetic tree for all possible exchanges of one amino acid with another. PFMT(Phylogenetic focused Mutation Tendency) matrix is different BLOSUM62 and PAM160 which are the most used scoring matrixes. This matrix calculates possibility of substitution from common ancestor to high spices. PFMT matrix scores substitution frequency in COGs databases which contain 152 KOGs's dataset. PFMT matrix usefully is able to compare between query sequence and sequences of more higher species and show detailed substitution relation of 20 amino acids.

• The Journal of the Korea Contents Association
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• v.12 no.3
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• pp.34-43
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• 2012

Determining the similarity between two strings can be applied various area such as information retrieval, spell checker and spam filtering. Similarity calculation between Korean strings based on dynamic programming methods firstly requires a definition of the similarity between phonemes. However, existing methods have a limitation that they use manually set similarity scores. In this paper, we propose a method to automatically calculate inter-phoneme similarity from a given set of variant words using a PAM-like probabilistic model. Our proposed method first finds the pairs of similar words from a given word set, and derives derivation rules from text alignment results among the similar word pairs. Then, similarity scores are calculated from the frequencies of variations between different phonemes. As an experimental result, we show an improvement of 10.1%~14.1% and 8.1%~11.8% in terms of sensitivity compared with the simple match-mismatch scoring scheme and the manually set inter-phoneme similarity scheme, respectively, with a specificity of 77.2%~80.4%.