A Method for Extracting Optimal Sequence Related to Biological Activity - ActiveSeqAnalyzerTN -

Tatsuya Nosho, Shigehiko Kanaya

Statistical techniques or some methods like as Expectation-maximization algorithm and Hidden Markov Model, were used to find the characteristic nucleotide pattern within DNA or RNA sequences that couldn't be found by applying multiple alignment techniques. But still there are many unanswered questions. And a comprehensive method that can relate Sequence to Biological activity or importance does not exist.
This software that enables us to solve some of these problems. And can extract the optimal sequence relating to biological activity, if we have the data composed of sequences and corresponding activity, regardless of definition of characteristic sequence.

Tadatoshi Sugio, Hideyuki Matsuura, Takeshi Matsui, Manabu Matsunaga, Tatsuya Nosho, Shigehiko Kanaya, Atsuhiko Shinmyo, and Ko Kato
Effect of the sequence context of the AUG initiation codon on the rate of translation in dicotyledonous and monocotyledonous plant cells. J. Biosci. Bioeng. (2009) in press

This software and its user manual is freely available at the present site. Java jdk5.0 is required to be installed in the user's computer to use this software.

Software download:ActiveSeqAnalyzerTN.zip
User Manual(Japanese):Manual(Japanese).pdf

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