Literature DB >> 12209144

Computational prediction of eukaryotic protein-coding genes.

Michael Q Zhang1.   

Abstract

The human genome sequence is the book of our life. Buried in this large volume are our genes, which are scattered as small DNA fragments throughout the genome and comprise a small percentage of the total text. Finding these indistinct 'needles' in a vast genomic 'haystack' can be extremely challenging. In response to this challenge, computational prediction approaches have proliferated in recent years that predict the location and structure of genes. Here, I discuss these approaches and explain why they have become essential for the analyses of newly sequenced genomes.

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Year:  2002        PMID: 12209144     DOI: 10.1038/nrg890

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  65 in total

1.  JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Authors:  Albin Sandelin; Wynand Alkema; Pär Engström; Wyeth W Wasserman; Boris Lenhard
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  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

3.  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

4.  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

5.  GeneWise and Genomewise.

Authors:  Ewan Birney; Michele Clamp; Richard Durbin
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

6.  EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches.

Authors:  Biju Issac; Gajendra Pal Singh Raghava
Journal:  Genome Res       Date:  2004-09       Impact factor: 9.043

7.  Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping.

Authors:  Ling-Hui Li; Jian-Chiuan Li; Yung-Feng Lin; Chung-Yen Lin; Chung-Yung Chen; Shih-Feng Tsai
Journal:  Nucleic Acids Res       Date:  2004-02-11       Impact factor: 16.971

8.  Gene and alternative splicing annotation with AIR.

Authors:  Liliana Florea; Valentina Di Francesco; Jason Miller; Russell Turner; Alison Yao; Michael Harris; Brian Walenz; Clark Mobarry; Gennady V Merkulov; Rosane Charlab; Ian Dew; Zuoming Deng; Sorin Istrail; Peter Li; Granger Sutton
Journal:  Genome Res       Date:  2005-01       Impact factor: 9.043

9.  A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

Authors:  Viktor Stolc; Lei Li; Xiangfeng Wang; Xueyong Li; Ning Su; Waraporn Tongprasit; Bin Han; Yongbiao Xue; Jiayang Li; Michael Snyder; Mark Gerstein; Jun Wang; Xing Wang Deng
Journal:  Plant Mol Biol       Date:  2005-09       Impact factor: 4.076

10.  Predicting aberrant CpG island methylation.

Authors:  F A Feltus; E K Lee; J F Costello; C Plass; P M Vertino
Journal:  Proc Natl Acad Sci U S A       Date:  2003-09-30       Impact factor: 11.205

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