Web サービス
- DDBJ Pipeline (サービス終了)
- GIB (2012.2 サービス終了)
- GIB-V (2012.2 サービス終了)
- GTPS (2012.2 サービス終了)
- FASTA (2010.3 サービス終了)
- PSI-BLSAT (2010.3 サービス終了)
- SSEARCH (2010.3 サービス終了)
- HMMPFAM (2010.3 サービス終了)
- H-Invitational Database CIB-DDBJ Flat File Server (2009.12.31 サービス終了)
- SRS (2008.12 サービス終了)
- LIBRA (2008.11 サービス終了)
- Lib score (2008.11 サービス終了)
- SQmatch (2008.11 サービス終了)
- PDB Retriever (2008.11 サービス終了)
- SSThread (2007.2 サービス終了)
- CAMUS (2007.02 サービス終了)
- S&W SEARCH (2006.04 サービス終了)
- malign (2005.9 サービス終了)
E-mail サーバによる検索解析
- get-entry
- get-version
- FASTA
- BLAST
- SSEARCH
- S\&WSEARCH
- ClustalW
- HMMPFAM
- malign
Reference
GIB
GIB-V
GTOP
- 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
Lib score
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