Introduction of My Research

Computational Biology

Conducted in Laboratory for Bioinformatics(Masaru Tomita's Lab.)

Keio Univesity Graduate School of Media and Governance (SFC)

Keywords: Computational Biology, Bioinformatics, Molecular biology, Computer Science, Statistics, DNA, RNA, Sequence analysis, AUG, ATG, Start codon, Translation initation, Ribosome binding sites, Kozak, Shine-Dalgarno, Ribosomes, CAP structure, Free energy, Processing, Artificial intelligence, AI, Logic programming, PROGOL, Knowledge discovery, Data mining, Neural networks

A living thing is formed by DNA. In the near future, whole human DNA sequences will be known. But even if the whole DNA sequence is known,it seems to be difficult to tell exactly how this life form would look by just looking at its DNA sequences. One of the current objectives of the research is to make a complete estimate of a life form from its DNA data. To do so, we will start analyzing DNA data by downloading it to our computer. Although it is only the first step to the complete estimation, some analysis is very difficult. And here, computer science may offer a great help to the analysis. For example, alignment algorithm helps us to estimate similarities between two or more sequences.

Researches

1. On negative selection against ATG triplets Near Start Codons (PP) J Mol Evol. 1999 Feb;48(2):213-217

2. Computer analyses of leaky scanning of AUG triplets in 5'UTR of vertebrate mRNAs

3.Computer Analyses of Translation Initiation Sites of M.genitalium.

4.Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various procaryotes. Yuko Osada, Rintaro Saito, Masaru Tomita. Bioinformatics 1999 Jul-Aug;15(7-8):578-81

5.Characteristic sequence pattern in the 5- to 20-bp upstream region of primate Alu elements Yoshimi Toda, Rintaro Saito, Masaru Tomita. J Mol Evol. 2000 Mar;50(3):232-7

6.Discovering knowledge from Translation Initiation Sites using Progol

7.Prediction of Translation Initiation Sites with neural networks

8.Analyses of whole genome suggest that many GTG start codons do not have strong SD sequences in Escherichia coli

9.Computer analyses of base forming potentials at both ends of rRNA operons in various genomes Gene(In press)

Tools

1.Calculation of annealing of two nucleic acid sequences

Data

1.Sequence features surrounding ORF start sites of completely sequenced bacteria

Surveys

1.Translation initiation in procaryotes

2.Translation initiation in eucaryotes

Links

Photos

If you have any question or comment, I will be very glad to receive an E-Mail from you.

E-Mail:rsaito@mag.keio.ac.jp

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