Literature DB >> 11222768

GeneSplicer: a new computational method for splice site prediction.

M Pertea1, X Lin, S L Salzberg.   

Abstract

GeneSplicer is a new, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been tested successfully using DNA from two reference organisms: the model plant Arabidopsis thaliana and human. It was compared to six programs representing the leading splice site detectors for each of these species: NetPlantGene, NetGene2, HSPL, NNSplice, GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational efficiency.

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Year:  2001        PMID： 11222768      PMCID： PMC29713          DOI： 10.1093/nar/29.5.1185

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


  12 in total

1.  EID: the Exon-Intron Database-an exhaustive database of protein-coding intron-containing genes.

Authors:  S Saxonov; I Daizadeh; A Fedorov; W Gilbert
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Improved splice site detection in Genie.

Authors:  M G Reese; F H Eeckman; D Kulp; D Haussler
Journal:  J Comput Biol       Date:  1997       Impact factor: 1.479

3.  Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.

Authors:  X Lin; S Kaul; S Rounsley; T P Shea; M I Benito; C D Town; C Y Fujii; T Mason; C L Bowman; M Barnstead; T V Feldblyum; C R Buell; K A Ketchum; J Lee; C M Ronning; H L Koo; K S Moffat; L A Cronin; M Shen; G Pai; S Van Aken; L Umayam; L J Tallon; J E Gill; M D Adams; A J Carrera; T H Creasy; H M Goodman; C R Somerville; G P Copenhaver; D Preuss; W C Nierman; O White; J A Eisen; S L Salzberg; C M Fraser; J C Venter
Journal:  Nature       Date:  1999-12-16       Impact factor: 49.962

4.  Interpolated Markov models for eukaryotic gene finding.

Authors:  S L Salzberg; M Pertea; A L Delcher; M J Gardner; H Tettelin
Journal:  Genomics       Date:  1999-07-01       Impact factor: 5.736

5.  Analysis of donor splice sites in different eukaryotic organisms.

Authors:  I B Rogozin; L Milanesi
Journal:  J Mol Evol       Date:  1997-07       Impact factor: 2.395

6.  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

Review 7.  Exon recognition in vertebrate splicing.

Authors:  S M Berget
Journal:  J Biol Chem       Date:  1995-02-10       Impact factor: 5.157

8.  Prediction of human mRNA donor and acceptor sites from the DNA sequence.

Authors:  S Brunak; J Engelbrecht; S Knudsen
Journal:  J Mol Biol       Date:  1991-07-05       Impact factor: 5.469

9.  Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.

Authors:  V V Solovyev; A A Salamov; C B Lawrence
Journal:  Nucleic Acids Res       Date:  1994-12-11       Impact factor: 16.971

10.  Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA.

Authors:  V Brendel; J Kleffe
Journal:  Nucleic Acids Res       Date:  1998-10-15       Impact factor: 16.971
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  183 in total

1.  DNA splice site detection: a comparison of specific and general methods.

Authors:  Won Kim; W John Wilbur
Journal:  Proc AMIA Symp       Date:  2002

2.  Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy.

Authors:  Christopher D Town; Foo Cheung; Rama Maiti; Jonathan Crabtree; Brian J Haas; Jennifer R Wortman; Erin E Hine; Ryan Althoff; Tamara S Arbogast; Luke J Tallon; Marielle Vigouroux; Martin Trick; Ian Bancroft
Journal:  Plant Cell       Date:  2006-04-21       Impact factor: 11.277

3.  Computational gene prediction using multiple sources of evidence.

Authors:  Jonathan E Allen; Mihaela Pertea; Steven L Salzberg
Journal:  Genome Res       Date:  2004-01       Impact factor: 9.043

4.  GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders.

Authors:  William H Majoros; Mihaela Pertea; Corina Antonescu; Steven L Salzberg
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

5.  Annotation of the Arabidopsis genome.

Authors:  Jennifer R Wortman; Brian J Haas; Linda I Hannick; Roger K Smith; Rama Maiti; Catherine M Ronning; Agnes P Chan; Chunhui Yu; Mulu Ayele; Catherine A Whitelaw; Owen R White; Christopher D Town
Journal:  Plant Physiol       Date:  2003-06       Impact factor: 8.340

Review 6.  Current methods of gene prediction, their strengths and weaknesses.

Authors:  Catherine Mathé; Marie-France Sagot; Thomas Schiex; Pierre Rouzé
Journal:  Nucleic Acids Res       Date:  2002-10-01       Impact factor: 16.971

Review 7.  Plasmid DNA vaccine vector design: impact on efficacy, safety and upstream production.

Authors:  James A Williams; Aaron E Carnes; Clague P Hodgson
Journal:  Biotechnol Adv       Date:  2009-02-20       Impact factor: 14.227

8.  Genome of bovine herpesvirus 5.

Authors:  G Delhon; M P Moraes; Z Lu; C L Afonso; E F Flores; R Weiblen; G F Kutish; D L Rock
Journal:  J Virol       Date:  2003-10       Impact factor: 5.103

9.  Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort.

Authors:  Raphaël Leman; Pascaline Gaildrat; Gérald Le Gac; Chandran Ka; Yann Fichou; Marie-Pierre Audrezet; Virginie Caux-Moncoutier; Sandrine M Caputo; Nadia Boutry-Kryza; Mélanie Léone; Sylvie Mazoyer; Françoise Bonnet-Dorion; Nicolas Sevenet; Marine Guillaud-Bataille; Etienne Rouleau; Brigitte Bressac-de Paillerets; Barbara Wappenschmidt; Maria Rossing; Danielle Muller; Violaine Bourdon; Françoise Revillon; Michael T Parsons; Antoine Rousselin; Grégoire Davy; Gaia Castelain; Laurent Castéra; Joanna Sokolowska; Florence Coulet; Capucine Delnatte; Claude Férec; Amanda B Spurdle; Alexandra Martins; Sophie Krieger; Claude Houdayer
Journal:  Nucleic Acids Res       Date:  2018-09-06       Impact factor: 16.971

10.  Assessment of the F9 genotype-specific FIX inhibitor risks and characterisation of 10 novel severe F9 defects in the first molecular series of Argentinian patients with haemophilia B.

Authors:  Claudia Pamela Radic; Liliana Carmen Rossetti; Miguel Martín Abelleyro; Miguel Candela; Raúl Pérez Bianco; Miguel de Tezanos Pinto; Irene Beatriz Larripa; Anne Goodeve; Carlos Daniel De Brasi
Journal:  Thromb Haemost       Date:  2012-10-23       Impact factor: 5.249
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