Literature DB >> 15215350

CHOP: visualization of 'wobbling' and isolation of highly conserved regions from aligned DNA sequences.

Masato Ohtsuka1, Shohei Horiuchi, Jerzy K Kulski, Minoru Kimura, Hidetoshi Inoko.   

Abstract

The web software CHOP was developed to visualize the 'wobbling' in the third codon position of aligned DNA sequences. The simple features of this tool allow users to easily find regions suspected of containing coding sequences (CDSs). The program also allows visualization of the nucleotide diversity between two genomic or gene sequences by graphically plotting the percentage identity between the two sequences. CHOP can also isolate highly conserved regions within both CDSs and non-CDSs. Highly conserved regions within CDSs include the regions with lower rates of synonymous substitution in which nucleotide sequences are expected to be under strong selective pressure. CHOP is available at http://bunsei2.med.u-tokai.ac.jp:8080/~ohtsuka/cds_finding.html.

Entities:  

Mesh：

Substances：

Year:  2004        PMID： 15215350      PMCID： PMC441586          DOI： 10.1093/nar/gkh448

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  7 in total

1.  PipMaker--a web server for aligning two genomic DNA sequences.

Authors:  S Schwartz; Z Zhang; K A Frazer; A Smit; C Riemer; J Bouck; R Gibbs; R Hardison; W Miller
Journal:  Genome Res       Date:  2000-04       Impact factor: 9.043

2.  The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study.

Authors:  Anton Nekrutenko; Kateryna D Makova; Wen-Hsiung Li
Journal:  Genome Res       Date:  2002-01       Impact factor: 9.043

3.  WABA success: a tool for sequence comparison between large genomes.

Authors:  D L Baillie; A M Rose
Journal:  Genome Res       Date:  2000-08       Impact factor: 9.043

4.  Initial sequencing and comparative analysis of the mouse genome.

Authors:  Robert H Waterston; Kerstin Lindblad-Toh; Ewan Birney; Jane Rogers; Josep F Abril; Pankaj Agarwal; Richa Agarwala; Rachel Ainscough; Marina Alexandersson; Peter An; Stylianos E Antonarakis; John Attwood; Robert Baertsch; Jonathon Bailey; Karen Barlow; Stephan Beck; Eric Berry; Bruce Birren; Toby Bloom; Peer Bork; Marc Botcherby; Nicolas Bray; Michael R Brent; Daniel G Brown; Stephen D Brown; Carol Bult; John Burton; Jonathan Butler; Robert D Campbell; Piero Carninci; Simon Cawley; Francesca Chiaromonte; Asif T Chinwalla; Deanna M Church; Michele Clamp; Christopher Clee; Francis S Collins; Lisa L Cook; Richard R Copley; Alan Coulson; Olivier Couronne; James Cuff; Val Curwen; Tim Cutts; Mark Daly; Robert David; Joy Davies; Kimberly D Delehaunty; Justin Deri; Emmanouil T Dermitzakis; Colin Dewey; Nicholas J Dickens; Mark Diekhans; Sheila Dodge; Inna Dubchak; Diane M Dunn; Sean R Eddy; Laura Elnitski; Richard D Emes; Pallavi Eswara; Eduardo Eyras; Adam Felsenfeld; Ginger A Fewell; Paul Flicek; Karen Foley; Wayne N Frankel; Lucinda A Fulton; Robert S Fulton; Terrence S Furey; Diane Gage; Richard A Gibbs; Gustavo Glusman; Sante Gnerre; Nick Goldman; Leo Goodstadt; Darren Grafham; Tina A Graves; Eric D Green; Simon Gregory; Roderic Guigó; Mark Guyer; Ross C Hardison; David Haussler; Yoshihide Hayashizaki; LaDeana W Hillier; Angela Hinrichs; Wratko Hlavina; Timothy Holzer; Fan Hsu; Axin Hua; Tim Hubbard; Adrienne Hunt; Ian Jackson; David B Jaffe; L Steven Johnson; Matthew Jones; Thomas A Jones; Ann Joy; Michael Kamal; Elinor K Karlsson; Donna Karolchik; Arkadiusz Kasprzyk; Jun Kawai; Evan Keibler; Cristyn Kells; W James Kent; Andrew Kirby; Diana L Kolbe; Ian Korf; Raju S Kucherlapati; Edward J Kulbokas; David Kulp; Tom Landers; J P Leger; Steven Leonard; Ivica Letunic; Rosie Levine; Jia Li; Ming Li; Christine Lloyd; Susan Lucas; Bin Ma; Donna R Maglott; Elaine R Mardis; Lucy Matthews; Evan Mauceli; John H Mayer; Megan McCarthy; W Richard McCombie; Stuart McLaren; Kirsten McLay; John D McPherson; Jim Meldrim; Beverley Meredith; Jill P Mesirov; Webb Miller; Tracie L Miner; Emmanuel Mongin; Kate T Montgomery; Michael Morgan; Richard Mott; James C Mullikin; Donna M Muzny; William E Nash; Joanne O Nelson; Michael N Nhan; Robert Nicol; Zemin Ning; Chad Nusbaum; Michael J O'Connor; Yasushi Okazaki; Karen Oliver; Emma Overton-Larty; Lior Pachter; Genís Parra; Kymberlie H Pepin; Jane Peterson; Pavel Pevzner; Robert Plumb; Craig S Pohl; Alex Poliakov; Tracy C Ponce; Chris P Ponting; Simon Potter; Michael Quail; Alexandre Reymond; Bruce A Roe; Krishna M Roskin; Edward M Rubin; Alistair G Rust; Ralph Santos; Victor Sapojnikov; Brian Schultz; Jörg Schultz; Matthias S Schwartz; Scott Schwartz; Carol Scott; Steven Seaman; Steve Searle; Ted Sharpe; Andrew Sheridan; Ratna Shownkeen; Sarah Sims; Jonathan B Singer; Guy Slater; Arian Smit; Douglas R Smith; Brian Spencer; Arne Stabenau; Nicole Stange-Thomann; Charles Sugnet; Mikita Suyama; Glenn Tesler; Johanna Thompson; David Torrents; Evanne Trevaskis; John Tromp; Catherine Ucla; Abel Ureta-Vidal; Jade P Vinson; Andrew C Von Niederhausern; Claire M Wade; Melanie Wall; Ryan J Weber; Robert B Weiss; Michael C Wendl; Anthony P West; Kris Wetterstrand; Raymond Wheeler; Simon Whelan; Jamey Wierzbowski; David Willey; Sophie Williams; Richard K Wilson; Eitan Winter; Kim C Worley; Dudley Wyman; Shan Yang; Shiaw-Pyng Yang; Evgeny M Zdobnov; Michael C Zody; Eric S Lander
Journal:  Nature       Date:  2002-12-05       Impact factor: 49.962

5.  ETOPE: Evolutionary test of predicted exons.

Authors:  Anton Nekrutenko; Wen-Yu Chung; Wen-Hsiung Li
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 6.  Medaka--a model organism from the far East.

Authors:  Joachim Wittbrodt; Akihiro Shima; Manfred Schartl
Journal:  Nat Rev Genet       Date:  2002-01       Impact factor: 53.242

7.  Comparative analysis of a 229-kb medaka genomic region, containing the zic1 and zic4 genes, with Fugu, human, and mouse.

Authors:  Masato Ohtsuka; Natsuko Kikuchi; Kenjiro Ozato; Hidetoshi Inoko; Minoru Kimura
Journal:  Genomics       Date:  2004-06       Impact factor: 5.736
  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.