Literature DB >> 8783942

Finding genes by computer: the state of the art.

J W Fickett1.   

Abstract

Discovering new genes, and their functions, can be aided not only by special purpose gene (and coding region) finding software, but also by searches in key databases, and by programs for finding particular sites relevant to gene expression, such as promoters and splice sites. No one software package includes all the necessary tools. I describe here the main kinds of tools; their working principles, strengths and limitations; and how combined evidence from multiple tools can aid in optimum gene identification.

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Year:  1996        PMID： 8783942     DOI： 10.1016/0168-9525(96)10038-x

Source DB:  PubMed          Journal:  Trends Genet        ISSN： 0168-9525            Impact factor:   11.639


  19 in total

1.  An assessment of gene prediction accuracy in large DNA sequences.

Authors:  R Guigó; P Agarwal; J F Abril; M Burset; J W Fickett
Journal:  Genome Res       Date:  2000-10       Impact factor: 9.043

2.  A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion.

Authors:  K Shirasu; A H Schulman; T Lahaye; P Schulze-Lefert
Journal:  Genome Res       Date:  2000-07       Impact factor: 9.043

3.  Gene structure prediction in syntenic DNA segments.

Authors:  Jonathan E Moore; James A Lake
Journal:  Nucleic Acids Res       Date:  2003-12-15       Impact factor: 16.971

Review 4.  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

5.  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

6.  Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.).

Authors:  Ranjeet R Kumar; Suneha Goswami; Sushil K Sharma; Yugal K Kala; Gyanendra K Rai; Dwijesh C Mishra; Monendra Grover; Gyanendra P Singh; Himanshu Pathak; Anil Rai; Viswanathan Chinnusamy; Raj D Rai
Journal:  OMICS       Date:  2015-09-25

7.  Measuring the coding potential of genomic sequences through a combination of triplet occurrence patterns and RNY preference.

Authors:  Christoforos Nikolaou; Yannis Almirantis
Journal:  J Mol Evol       Date:  2004-09       Impact factor: 2.395

8.  A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome.

Authors:  R Panstruga; R Büschges; P Piffanelli; P Schulze-Lefert
Journal:  Nucleic Acids Res       Date:  1998-02-15       Impact factor: 16.971

9.  BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.

Authors:  Wenming Zhao; Jing Wang; Ximiao He; Xiaobing Huang; Yongzhi Jiao; Mingtao Dai; Shulin Wei; Jian Fu; Ye Chen; Xiaoyu Ren; Yong Zhang; Peixiang Ni; Jianguo Zhang; Songgang Li; Jian Wang; Gane Ka-Shu Wong; Hongyu Zhao; Jun Yu; Huanming Yang; Jun Wang
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

10.  Intraspecific variability of the tandem repeats in Nicotiana putrescine N-methyltransferases.

Authors:  T Hashimoto; T Shoji; T Mihara; H Oguri; K Tamaki; K Suzuki; Y Yamada
Journal:  Plant Mol Biol       Date:  1998-05       Impact factor: 4.076
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