메뉴 건너뛰기




Volumn 35, Issue SUPPL.2, 2007, Pages

PROMALS web server for accurate multiple protein sequence alignments

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 34547590429     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm227     Document Type: Article
Times cited : (58)

References (23)
  • 2
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G. and Gibson, T.J. (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, 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 3
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson, J.D., Plewniak, F. and Poch, O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 4
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 5
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh, K., Kuma, K., Toh, H. and Miyata, T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res., 33, 511-518.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 6
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., Higgins, D.G. and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 7
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • Do, C.B., Mahabhashyam, M.S., Brudno, M. and Batzoglou, S. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
    • (2005) Genome Res. , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3    Batzoglou, S.4
  • 8
    • 33750001271 scopus 로고    scopus 로고
    • MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information
    • Pei, J. and Grishin, N.V. (2006) MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res., 34, 4364-4374.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 4364-4374
    • Pei, J.1    Grishin, N.V.2
  • 9
    • 23144440940 scopus 로고    scopus 로고
    • PRALINE: A multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
    • Simossis, V.A. and Heringa, J. (2005) PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res., 33, W289-W294.
    • (2005) Nucleic Acids Res. , vol.33
    • Simossis, V.A.1    Heringa, J.2
  • 10
    • 0034255358 scopus 로고    scopus 로고
    • DbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches
    • Thompson, J.D., Plewniak, F., Thierry, J. and Poch, O. (2000) DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res., 28, 2919-2926.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2919-2926
    • Thompson, J.D.1    Plewniak, F.2    Thierry, J.3    Poch, O.4
  • 11
    • 2942619012 scopus 로고    scopus 로고
    • 3DCoffee: Combining protein sequences and structures within multiple sequence alignments
    • O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D.G. and Notredame, C. (2004) 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol., 340, 385-395.
    • (2004) J. Mol. Biol. , vol.340 , pp. 385-395
    • O'Sullivan, O.1    Suhre, K.2    Abergel, C.3    Higgins, D.G.4    Notredame, C.5
  • 12
    • 34248532415 scopus 로고    scopus 로고
    • PROMALS: Towards accurate multiple sequence alignments of distantly related sequences
    • doi: 10.1093/bioinformatics/btm017
    • Pei, J. and Grishin, N.V. (2007) PROMALS: towards accurate multiple sequence alignments of distantly related sequences. Bioinformatics doi: 10.1093/bioinformatics/btm017.
    • (2007) Bioinformatics
    • Pei, J.1    Grishin, N.V.2
  • 13
    • 24644512819 scopus 로고    scopus 로고
    • SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures
    • Zhou, H. and Zhou, Y. (2005) SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics, 21, 3615-3621.
    • (2005) Bioinformatics , vol.21 , pp. 3615-3621
    • Zhou, H.1    Zhou, Y.2
  • 14
    • 0037433034 scopus 로고    scopus 로고
    • PCMA: Fast and accurate multiple sequence alignment based on profile consistency
    • Pei, J., Sadreyev, R. and Grishin, N.V. (2003) PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics, 19, 427-428.
    • (2003) Bioinformatics , vol.19 , pp. 427-428
    • Pei, J.1    Sadreyev, R.2    Grishin, N.V.3
  • 15
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 18
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 19
    • 16344394781 scopus 로고    scopus 로고
    • SABmark-a benchmark for sequence alignment that covers the entire known fold space
    • Van Walle, I., Lasters, I. and Wyns, L. (2005) SABmark-a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics, 21, 1267-1268.
    • (2005) Bioinformatics , vol.21 , pp. 1267-1268
    • Van Walle, I.1    Lasters, I.2    Wyns, L.3
  • 21
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 22
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: Calculation of positional conservation in a protein sequence alignment
    • Pei, J. and Grishin, N.V. (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17, 700-712.
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.