Literature DB >> 10068696

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.

J D Thompson1, F Plewniak, O Poch.   

Abstract

SUMMARY: BAliBASE is a database of manually refined multiple sequence alignments categorized by core blocks of conservation sequence length, similarity, and the presence of insertions and N/C-terminal extensions. AVAILABILITY: From http://www-igbmc. u-strasbg.fr/BioInfo/BAliBASE/index.html

Mesh：

Year:  1999        PMID： 10068696     DOI： 10.1093/bioinformatics/15.1.87

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  100 in total

1.  BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.

Authors:  A Bahr; J D Thompson; J C Thierry; O Poch
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.

Authors:  J D Thompson; F Plewniak; J Thierry; O Poch
Journal:  Nucleic Acids Res       Date:  2000-08-01       Impact factor: 16.971

3.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

Authors:  Kazutaka Katoh; Kazuharu Misawa; Kei-ichi Kuma; Takashi Miyata
Journal:  Nucleic Acids Res       Date:  2002-07-15       Impact factor: 16.971

4.  HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database.

Authors:  Lucy A Stebbings; Kenji Mizuguchi
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.

Authors:  Olivier Poirot; Karsten Suhre; Chantal Abergel; Eamonn O'Toole; Cedric Notredame
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

6.  DIALIGN: multiple DNA and protein sequence alignment at BiBiServ.

Authors:  Burkhard Morgenstern
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

7.  MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Authors:  Robert C Edgar
Journal:  Nucleic Acids Res       Date:  2004-03-19       Impact factor: 16.971

8.  An assessment of substitution scores for protein profile-profile comparison.

Authors:  Xugang Ye; Guoli Wang; Stephen F Altschul
Journal:  Bioinformatics       Date:  2011-10-13       Impact factor: 6.937

9.  Aligning protein sequence and analysing substitution pattern using a class-specific matrix.

Authors:  Hai Song Xu; Wen Ke Ren; Xiao Hui Liu; Xiao Qin Li
Journal:  J Biosci       Date:  2010-06       Impact factor: 1.826

10.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Authors:  Sarel J Fleishman; Timothy A Whitehead; Eva-Maria Strauch; Jacob E Corn; Sanbo Qin; Huan-Xiang Zhou; Julie C Mitchell; Omar N A Demerdash; Mayuko Takeda-Shitaka; Genki Terashi; Iain H Moal; Xiaofan Li; Paul A Bates; Martin Zacharias; Hahnbeom Park; Jun-su Ko; Hasup Lee; Chaok Seok; Thomas Bourquard; Julie Bernauer; Anne Poupon; Jérôme Azé; Seren Soner; Sefik Kerem Ovali; Pemra Ozbek; Nir Ben Tal; Türkan Haliloglu; Howook Hwang; Thom Vreven; Brian G Pierce; Zhiping Weng; Laura Pérez-Cano; Carles Pons; Juan Fernández-Recio; Fan Jiang; Feng Yang; Xinqi Gong; Libin Cao; Xianjin Xu; Bin Liu; Panwen Wang; Chunhua Li; Cunxin Wang; Charles H Robert; Mainak Guharoy; Shiyong Liu; Yangyu Huang; Lin Li; Dachuan Guo; Ying Chen; Yi Xiao; Nir London; Zohar Itzhaki; Ora Schueler-Furman; Yuval Inbar; Vladimir Potapov; Mati Cohen; Gideon Schreiber; Yuko Tsuchiya; Eiji Kanamori; Daron M Standley; Haruki Nakamura; Kengo Kinoshita; Camden M Driggers; Robert G Hall; Jessica L Morgan; Victor L Hsu; Jian Zhan; Yuedong Yang; Yaoqi Zhou; Panagiotis L Kastritis; Alexandre M J J Bonvin; Weiyi Zhang; Carlos J Camacho; Krishna P Kilambi; Aroop Sircar; Jeffrey J Gray; Masahito Ohue; Nobuyuki Uchikoga; Yuri Matsuzaki; Takashi Ishida; Yutaka Akiyama; Raed Khashan; Stephen Bush; Denis Fouches; Alexander Tropsha; Juan Esquivel-Rodríguez; Daisuke Kihara; P Benjamin Stranges; Ron Jacak; Brian Kuhlman; Sheng-You Huang; Xiaoqin Zou; Shoshana J Wodak; Joel Janin; David Baker
Journal:  J Mol Biol       Date:  2011-09-29       Impact factor: 5.469
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