Literature DB >> 12824355

SLAM web server for comparative gene finding and alignment.

Simon Cawley1, Lior Pachter, Marina Alexandersson.   

Abstract

SLAM is a program that simultaneously aligns and annotates pairs of homologous sequences. The SLAM web server integrates SLAM with repeat masking tools and the AVID alignment program to allow for rapid alignment and gene prediction in user submitted sequences. Along with annotations and alignments for the submitted sequences, users obtain a list of predicted conserved non-coding sequences (and their associated alignments). The web site also links to whole genome annotations of the human, mouse and rat genomes produced with the SLAM program. The server can be accessed at http://bio.math.berkeley.edu/slam.

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Year:  2003        PMID： 12824355      PMCID： PMC168989          DOI： 10.1093/nar/gkg583

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


  11 in total

1.  Integrating genomic homology into gene structure prediction.

Authors:  I Korf; P Flicek; D Duan; M R Brent
Journal:  Bioinformatics       Date:  2001       Impact factor: 6.937

2.  Applications of generalized pair hidden Markov models to alignment and gene finding problems.

Authors:  Lior Pachter; Marina Alexandersson; Simon Cawley
Journal:  J Comput Biol       Date:  2002       Impact factor: 1.479

3.  A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.

Authors:  Richard J Mural; Mark D Adams; Eugene W Myers; Hamilton O Smith; George L Gabor Miklos; Ron Wides; Aaron Halpern; Peter W Li; Granger G Sutton; Joe Nadeau; Steven L Salzberg; Robert A Holt; Chinnappa D Kodira; Fu Lu; Lin Chen; Zuoming Deng; Carlos C Evangelista; Weiniu Gan; Thomas J Heiman; Jiayin Li; Zhenya Li; Gennady V Merkulov; Natalia V Milshina; Ashwinikumar K Naik; Rong Qi; Bixiong Chris Shue; Aihui Wang; Jian Wang; Xin Wang; Xianghe Yan; Jane Ye; Shibu Yooseph; Qi Zhao; Liansheng Zheng; Shiaoping C Zhu; Kendra Biddick; Randall Bolanos; Arthur L Delcher; Ian M Dew; Daniel Fasulo; Michael J Flanigan; Daniel H Huson; Saul A Kravitz; Jason R Miller; Clark M Mobarry; Knut Reinert; Karin A Remington; Qing Zhang; Xiangqun H Zheng; Deborah R Nusskern; Zhongwu Lai; Yiding Lei; Wenyan Zhong; Alison Yao; Ping Guan; Rui-Ru Ji; Zhiping Gu; Zhen-Yuan Wang; Fei Zhong; Chunlin Xiao; Chia-Chien Chiang; Mark Yandell; Jennifer R Wortman; Peter G Amanatides; Suzanne L Hladun; Eric C Pratts; Jeffery E Johnson; Kristina L Dodson; Kerry J Woodford; Cheryl A Evans; Barry Gropman; Douglas B Rusch; Eli Venter; Mei Wang; Thomas J Smith; Jarrett T Houck; Donald E Tompkins; Charles Haynes; Debbie Jacob; Soo H Chin; David R Allen; Carl E Dahlke; Robert Sanders; Kelvin Li; Xiangjun Liu; Alexander A Levitsky; William H Majoros; Quan Chen; Ashley C Xia; John R Lopez; Michael T Donnelly; Matthew H Newman; Anna Glodek; Cheryl L Kraft; Marc Nodell; Feroze Ali; Hui-Jin An; Danita Baldwin-Pitts; Karen Y Beeson; Shuang Cai; Mark Carnes; Amy Carver; Parris M Caulk; Angela Center; Yen-Hui Chen; Ming-Lai Cheng; My D Coyne; Michelle Crowder; Steven Danaher; Lionel B Davenport; Raymond Desilets; Susanne M Dietz; Lisa Doup; Patrick Dullaghan; Steven Ferriera; Carl R Fosler; Harold C Gire; Andres Gluecksmann; Jeannine D Gocayne; Jonathan Gray; Brit Hart; Jason Haynes; Jeffery Hoover; Tim Howland; Chinyere Ibegwam; Mena Jalali; David Johns; Leslie Kline; Daniel S Ma; Steven MacCawley; Anand Magoon; Felecia Mann; David May; Tina C McIntosh; Somil Mehta; Linda Moy; Mee C Moy; Brian J Murphy; Sean D Murphy; Keith A Nelson; Zubeda Nuri; Kimberly A Parker; Alexandre C Prudhomme; Vinita N Puri; Hina Qureshi; John C Raley; Matthew S Reardon; Megan A Regier; Yu-Hui C Rogers; Deanna L Romblad; Jakob Schutz; John L Scott; Richard Scott; Cynthia D Sitter; Michella Smallwood; Arlan C Sprague; Erin Stewart; Renee V Strong; Ellen Suh; Karena Sylvester; Reginald Thomas; Ni Ni Tint; Christopher Tsonis; Gary Wang; George Wang; Monica S Williams; Sherita M Williams; Sandra M Windsor; Keriellen Wolfe; Mitchell M Wu; Jayshree Zaveri; Kabir Chaturvedi; Andrei E Gabrielian; Zhaoxi Ke; Jingtao Sun; Gangadharan Subramanian; J Craig Venter; Cynthia M Pfannkoch; Mary Barnstead; Lisa D Stephenson
Journal:  Science       Date:  2002-05-31       Impact factor: 47.728

4.  SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.

Authors:  Marina Alexandersson; Simon Cawley; Lior Pachter
Journal:  Genome Res       Date:  2003-03       Impact factor: 9.043

5.  Comparative gene prediction in human and mouse.

Authors:  Genís Parra; Pankaj Agarwal; Josep F Abril; Thomas Wiehe; James W Fickett; Roderic Guigó
Journal:  Genome Res       Date:  2003-01       Impact factor: 9.043

6.  AVID: A global alignment program.

Authors:  Nick Bray; Inna Dubchak; Lior Pachter
Journal:  Genome Res       Date:  2003-01       Impact factor: 9.043

7.  The UCSC Genome Browser Database.

Authors:  D Karolchik; R Baertsch; M Diekhans; T S Furey; A Hinrichs; Y T Lu; K M Roskin; M Schwartz; C W Sugnet; D J Thomas; R J Weber; D Haussler; W J Kent
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

8.  Genie--gene finding in Drosophila melanogaster.

Authors:  M G Reese; D Kulp; H Tammana; D Haussler
Journal:  Genome Res       Date:  2000-04       Impact factor: 9.043

9.  Prediction of complete gene structures in human genomic DNA.

Authors:  C Burge; S Karlin
Journal:  J Mol Biol       Date:  1997-04-25       Impact factor: 5.469

10.  Human and mouse gene structure: comparative analysis and application to exon prediction.

Authors:  S Batzoglou; L Pachter; J P Mesirov; B Berger; E S Lander
Journal:  Genome Res       Date:  2000-07       Impact factor: 9.043
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  5 in total

1.  AUGUSTUS: a web server for gene finding in eukaryotes.

Authors:  Mario Stanke; Rasmus Steinkamp; Stephan Waack; Burkhard Morgenstern
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  Meeting report: a workshop on Best Practices in Genome Annotation.

Authors:  Ramana Madupu; Lauren M Brinkac; Jennifer Harrow; Laurens G Wilming; Ulrike Böhme; Philippe Lamesch; Linda I Hannick
Journal:  Database (Oxford)       Date:  2010-02-18       Impact factor: 3.451

3.  Testing the coding potential of conserved short genomic sequences.

Authors:  Jing Wu
Journal:  Adv Bioinformatics       Date:  2010-03-08

Review 4.  EGASP: the human ENCODE Genome Annotation Assessment Project.

Authors:  Roderic Guigó; Paul Flicek; Josep F Abril; Alexandre Reymond; Julien Lagarde; France Denoeud; Stylianos Antonarakis; Michael Ashburner; Vladimir B Bajic; Ewan Birney; Robert Castelo; Eduardo Eyras; Catherine Ucla; Thomas R Gingeras; Jennifer Harrow; Tim Hubbard; Suzanna E Lewis; Martin G Reese
Journal:  Genome Biol       Date:  2006-08-07       Impact factor: 13.583

5.  Improving the specificity of exon prediction using comparative genomics.

Authors:  Jing Wu
Journal:  BMC Genomics       Date:  2008-09-16       Impact factor: 3.969
  5 in total

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