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Reference
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Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures.
Nakashima H, Fukuchi S, Nishikawa K
J Biochem 2003 Apr;133(4):507-13. Pubmed: 12761299
Unique amino acid composition of proteins in halophilic bacteria.
Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K
J Mol Biol 2003 Mar 21;327(2):347-57. Pubmed: 12628242
Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins.
Fukami-Kobayashi K, Tateno Y, Nishikawa K Mol Biol Evol 2003 Feb;20(2):267-77. Pubmed: 12598694
A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome.
Homma K, Fukuchi S, Kawabata T, Ota M, Nishikawa K Gene 2002 Jul 10;294(1-2):25-33. Pubmed: 12234664
GTOP: a database of protein structures predicted from genome sequences.
Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N, Nishikawa K Nucleic Acids Res 2002 Jan 1;30(1):294-8. Pubmed: 11752318
Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches.
Kawabata T, Arisaka F, Nishikawa K Gene 2000 Dec 23;259(1-2):223-33. Pubmed: 11163980
GIPS
HMMPFAM
LIBRA
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DDBJ Pipeline
DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data Nagasaki H, Mochizuki T, Kodama Y, Saruhashi S, Morizaki S, Sugawara H, Ohyanagi H, Kurata N, Okubo K, Takagi T, Kaminuma E, Nakamura Y. DNA Res. 2013 Aug;20(4):383-90. Pubmed: 23657089
PSI-BLAST
SSEARCH
WINA
Identification of regions in which positive selection may operate in S-RNase of Rosaceae: implication for S-allele-specific recognition sites in S-RNase.
Ishimizu T, Endo T, Yamaguchi-Kabata Y, Nakamura KT, Sakiyama F, Norioka S FEBS Lett 1998 Dec 4;440(3):337-42. Pubmed: 9872398
Large-scale search for genes on which positive selection may operate.
Endo T, Ikeo K, Gojobori T Mol Biol Evol 1996 May;13(5):685-90. Pubmed: 8676743
Reduction of synonymous substitutions in the core protein gene of hepatitis C virus.
Ina Y, Mizokami M, Ohba K, Gojobori T J Mol Evol 1994 Jan;38(1):50-6. Pubmed: 8151715
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
Nei M, Gojobori T Mol Biol Evol 1986 Sep;3(5):418-26. Pubmed: 3444411