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[TEST130219]検索解析サービス References

jukohira — Tue, 19 Feb 2013 03:32:38 +0000

DDBJ のサービス全般に関連して
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原著論文および関連論文
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DDBJ のサービス全般に関連して

DDBJ HP

参考書

「DDBJ の利用法」
五條堀孝・菅原秀明編著（共立出版）
「DDBJ の利用法」補助資料
「あなたにも役立つバイオインフォマティクス」
菅原秀明編（共立出版）
「分子生物学のためのバイオインフォマティクス入門」
J.C.Setubal, J.Medicanis 著／五條堀孝　監訳（共立出版）
「バイオデータベースとウェブツールの手とり足とり活用法」改訂　第２版
中村保一，他編（羊土社）

現在公開中の各 WWW サービスのHelp

原著論文および関連論文

FASTA

原著論文

Pearson WR, Lipman DJ. (1988) Improved tools for biological sequence
comparison. Proc Natl Acad Sci U S A. 85(8):2444-8.
Lipman DJ, Pearson WR. (1985) Rapid and sensitive protein similarity
searches. Science. 227(4693):1435-41.

関連論文

Wilbur WJ, Lipman DJ. (1983) Rapid similarity searches of nucleic
acid and protein data banks. Proc Natl Acad Sci U S A. 80(3):726-30.

BLAST

原著論文

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W,
Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein
database search programs. Nucleic Acids Res. 25(17):3389-402.

関連論文

Zhang J, Madden TL. (1997) PowerBLAST: a new network BLAST application
for interactive or automated sequence analysis and annotation. Genome Res.
7(6):649-56.
Madden TL, Tatusov RL, Zhang J. (1996) Applications of network BLAST
server. Methods Enzymol. 266:131-41.
Gish W, States DJ. (1993) Identification of protein coding regions by
database similarity search. Nat Genet. 3(3):266-72.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local
alignment search tool. J Mol Biol. 215(3):403-10.
Karlin S, Altschul SF. (1990) Methods for assessing the statistical
significance of molecular sequence features by using general scoring
schemes. Proc Natl Acad Sci U S A. 87(6):2264-8.

PSI-BLAST

原著論文

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W,
Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein
database search programs. Nucleic Acids Res. 25(17):3389-402.

SSEARCH

原著論文

Smith TF, Waterman MS. (1981) Comparison of biosequences. Adv. Appl. Math. 2:482-9.
Smith TF, Waterman MS. (1981) Identification of common molecular subsequences. J Mol Biol. 147(1):195-7.

関連論文

Pearson WR, Lipman DJ. (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 85(8):2444-8.
Lipman DJ, Pearson WR. (1985) Rapid and sensitive protein similarity searches. Science. 227(4693):1435-41.

HMMPFAM

原著論文

Sonnhammer EL, Eddy SR, Durbin R. (1997) Pfam: A Comprehensive Database of Protein Families Based on Seed Alignments. Proteins, 28:405-420
Eddy SR. (1998) Profile Hidden Markov Models. Bioinformatics, 14:755-763

ClustalW

原著論文

Thompson JD, Higgins DG, Gibson TJ. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Nucleic Acids Res. 22(22):4673-80.

関連論文

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31(13):3497-500.

GIB

原著論文

Fumoto M, Miyazaki S, Sugawara H. (2002) Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more. Nucleic Acids Res. 30(1):66-8.

GIB-V

原著論文

Hirahata M, Abe T, Tanaka N, Kuwana Y, Shigemoto Y, Miyazaki S, Suzuki Y, Sugawara H.(2007) Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes. Nucleic Acids Res. 2007 Jan;35(Database issue):D339-42.

GTPS

原論文

Kosuge T, Abe T, Okido T, Tanaka N, Hirahata M, Maruyama Y, Mashima J, Tomiki A, Kurokawa M, Himeno R, Fukuchi S, Miyazaki S, Gojobori T, Tateno Y, Sugawara H. (2006) Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS). DNA Res. 2006 Dec 31;13(6):245-54.

GTOP

原著論文

Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N, Nishikawa K. (2002) GTOP: a database of protein structures predicted from genome sequences. Nucleic Acids Res. 30(1):294-8.

関連論文

Fukami-Kobayashi K, Tateno Y, Nishikawa K. (2003) Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins. Mol Biol Evol. 20(2):267-77.
Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K. (2003) Unique amino acid composition of proteins in halophilic bacteria. J Mol Biol. 327(2):347-57.
Nakashima H, Fukuchi S, Nishikawa K. (2003) Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem (Tokyo). 133(4):507-13.
Homma K, Fukuchi S, Kawabata T, Ota M, Nishikawa K. (2002) A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome. Gene. 294(1-2):25-33.
Kawabata T, Arisaka F, Nishikawa K. (2000) Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database
searches. Gene. 259(1-2):223-33.

LIBRA

原著論文

Ota M, Nishikawa K. (1999) Feasibility in the inverse protein folding protocol. Protein Sci. 8(5):1001-9.

関連論文

Ota M, Isogai Y, Nishikawa K. (1997) Structural requirement of highly-conserved residues in globins. FEBS Lett. 415(2):129-33.
Ota M, Nishikawa K. (1997) Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of
proteins. Protein Eng. 10(4):339-51.
Ota M, Kanaya S, Nishikawa K. (1995) Desk-top analysis of the structural stability of various point mutations introduced into ribonuclease H. J Mol Biol. 248(4):733-8.

Lib score

原著論文

Udaka K, Wiesmuller KH, Kienle S, Jung G, Tamamura H, Yamagishi H, Okumura K, Walden P, Suto T, Kawasaki T. (2000) An tomated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries. Immunogenetics. 51(10):816-28.

WINA

原著論文

Endo T, Ikeo K, Gojobori T. (1996) Large-scale search for genes on which positive selection may operate. Mol Biol Evol. 13(5):685-90.

関連論文

Ishimizu T, Endo T, Yamaguchi-Kabata Y, Nakamura KT, Sakiyama F, Norioka S. (1998) Identification of regions in which positive selection may operate in S-RNase of Rosaceae: implication for S-allele-specific recognition sites in S-RNase. FEBS Lett. 440(3):337-42.
Nei M, Gojobori T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 3(5):418-26.
Ina Y, Mizokami M, Ohba K, Gojobori T. (1994) Reduction of synonymous substitutions in the core protein gene of hepatitis C virus. J Mol Evol. 38(1):50-6.

検索解析サービス References

admin — Mon, 30 Aug 2010 07:48:54 +0000

DDBJ のサービス全般に関連して
現在公開中の各 WWW サービスの Help
原著論文および関連論文
アーカイブ

DDBJ のサービス全般に関連して

DDBJ HP

参考書

「DDBJ の利用法」
五條堀孝・菅原秀明編著（共立出版）
「DDBJ の利用法」補助資料
「あなたにも役立つバイオインフォマティクス」
菅原秀明編（共立出版）
「分子生物学のためのバイオインフォマティクス入門」
J.C.Setubal, J.Medicanis 著／五條堀孝　監訳（共立出版）
「バイオデータベースとウェブツールの手とり足とり活用法」改訂　第２版
中村保一，他編（羊土社）

現在公開中の各 WWW サービスのHelp

原著論文および関連論文

FASTA

原著論文

Pearson WR, Lipman DJ. (1988) Improved tools for biological sequence
comparison. Proc Natl Acad Sci U S A. 85(8):2444-8.
Lipman DJ, Pearson WR. (1985) Rapid and sensitive protein similarity
searches. Science. 227(4693):1435-41.

関連論文

Wilbur WJ, Lipman DJ. (1983) Rapid similarity searches of nucleic
acid and protein data banks. Proc Natl Acad Sci U S A. 80(3):726-30.

BLAST

原著論文

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W,
Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein
database search programs. Nucleic Acids Res. 25(17):3389-402.

関連論文

Zhang J, Madden TL. (1997) PowerBLAST: a new network BLAST application
for interactive or automated sequence analysis and annotation. Genome Res.
7(6):649-56.
Madden TL, Tatusov RL, Zhang J. (1996) Applications of network BLAST
server. Methods Enzymol. 266:131-41.
Gish W, States DJ. (1993) Identification of protein coding regions by
database similarity search. Nat Genet. 3(3):266-72.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local
alignment search tool. J Mol Biol. 215(3):403-10.
Karlin S, Altschul SF. (1990) Methods for assessing the statistical
significance of molecular sequence features by using general scoring
schemes. Proc Natl Acad Sci U S A. 87(6):2264-8.

PSI-BLAST

原著論文

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W,
Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein
database search programs. Nucleic Acids Res. 25(17):3389-402.

SSEARCH

原著論文

Smith TF, Waterman MS. (1981) Comparison of biosequences. Adv. Appl. Math. 2:482-9.
Smith TF, Waterman MS. (1981) Identification of common molecular subsequences. J Mol Biol. 147(1):195-7.

関連論文

Pearson WR, Lipman DJ. (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 85(8):2444-8.
Lipman DJ, Pearson WR. (1985) Rapid and sensitive protein similarity searches. Science. 227(4693):1435-41.

HMMPFAM

原著論文

Sonnhammer EL, Eddy SR, Durbin R. (1997) Pfam: A Comprehensive Database of Protein Families Based on Seed Alignments. Proteins, 28:405-420
Eddy SR. (1998) Profile Hidden Markov Models. Bioinformatics, 14:755-763

ClustalW

原著論文

Thompson JD, Higgins DG, Gibson TJ. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Nucleic Acids Res. 22(22):4673-80.

関連論文

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31(13):3497-500.

GIB

原著論文

Fumoto M, Miyazaki S, Sugawara H. (2002) Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more. Nucleic Acids Res. 30(1):66-8.

GIB-V

原著論文

Hirahata M, Abe T, Tanaka N, Kuwana Y, Shigemoto Y, Miyazaki S, Suzuki Y, Sugawara H.(2007) Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes. Nucleic Acids Res. 2007 Jan;35(Database issue):D339-42.

GTPS

原論文

Kosuge T, Abe T, Okido T, Tanaka N, Hirahata M, Maruyama Y, Mashima J, Tomiki A, Kurokawa M, Himeno R, Fukuchi S, Miyazaki S, Gojobori T, Tateno Y, Sugawara H. (2006) Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS). DNA Res. 2006 Dec 31;13(6):245-54.

GTOP

原著論文

Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N, Nishikawa K. (2002) GTOP: a database of protein structures predicted from genome sequences. Nucleic Acids Res. 30(1):294-8.

関連論文

Fukami-Kobayashi K, Tateno Y, Nishikawa K. (2003) Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins. Mol Biol Evol. 20(2):267-77.
Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K. (2003) Unique amino acid composition of proteins in halophilic bacteria. J Mol Biol. 327(2):347-57.
Nakashima H, Fukuchi S, Nishikawa K. (2003) Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem (Tokyo). 133(4):507-13.
Homma K, Fukuchi S, Kawabata T, Ota M, Nishikawa K. (2002) A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome. Gene. 294(1-2):25-33.
Kawabata T, Arisaka F, Nishikawa K. (2000) Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database
searches. Gene. 259(1-2):223-33.

LIBRA

原著論文

Ota M, Nishikawa K. (1999) Feasibility in the inverse protein folding protocol. Protein Sci. 8(5):1001-9.

関連論文

Ota M, Isogai Y, Nishikawa K. (1997) Structural requirement of highly-conserved residues in globins. FEBS Lett. 415(2):129-33.
Ota M, Nishikawa K. (1997) Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of
proteins. Protein Eng. 10(4):339-51.
Ota M, Kanaya S, Nishikawa K. (1995) Desk-top analysis of the structural stability of various point mutations introduced into ribonuclease H. J Mol Biol. 248(4):733-8.

Lib score

原著論文

Udaka K, Wiesmuller KH, Kienle S, Jung G, Tamamura H, Yamagishi H, Okumura K, Walden P, Suto T, Kawasaki T. (2000) An tomated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries. Immunogenetics. 51(10):816-28.

WINA

原著論文

Endo T, Ikeo K, Gojobori T. (1996) Large-scale search for genes on which positive selection may operate. Mol Biol Evol. 13(5):685-90.

関連論文

Ishimizu T, Endo T, Yamaguchi-Kabata Y, Nakamura KT, Sakiyama F, Norioka S. (1998) Identification of regions in which positive selection may operate in S-RNase of Rosaceae: implication for S-allele-specific recognition sites in S-RNase. FEBS Lett. 440(3):337-42.
Nei M, Gojobori T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 3(5):418-26.
Ina Y, Mizokami M, Ohba K, Gojobori T. (1994) Reduction of synonymous substitutions in the core protein gene of hepatitis C virus. J Mol Evol. 38(1):50-6.

DDBJ » Search Results » archives/email_doc-j.html

[TEST130219]検索解析サービス References

DDBJ のサービス全般に関連して

DDBJ HP

参考書

現在公開中の各 WWW サービスのHelp

原著論文および関連論文

FASTA

BLAST

PSI-BLAST

SSEARCH

HMMPFAM

ClustalW

GIB

GIB-V

GTPS

GTOP

LIBRA

Lib score

WINA

アーカイブ

各種参考文献・資料等

Web サービスのHelp（一部サービス終了）

E-mail サーバの解説（サービス終了）

検索解析サービス References

DDBJ のサービス全般に関連して

DDBJ HP

参考書

現在公開中の各 WWW サービスのHelp

原著論文および関連論文

FASTA

BLAST

PSI-BLAST

SSEARCH

HMMPFAM

ClustalW

GIB

GIB-V

GTPS

GTOP

LIBRA

Lib score

WINA

アーカイブ

各種参考文献・資料等

Web サービスのHelp（一部サービス終了）

E-mail サーバの解説（サービス終了）