Literature DB >> 16749184

The gene identification problem: an overview for developers.

J W Fickett1.   

Abstract

The gene identification problem is the problem of interpreting nucleotide sequences by computer, in order to provide tentative annotation on the location, structure, and functional class of protein-coding genes. This problem is of self-evident importance, and is far from being fully solved, particularly for higher eukaryotes. Thus it is not surprising that the number of algorithm and software developers working in the area is rapidly increasing. The present paper is an overview of the field, with an emphasis on eukaryotes, for such developers.

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Year:  1996        PMID: 16749184     DOI: 10.1016/s0097-8485(96)80012-x

Source DB:  PubMed          Journal:  Comput Chem        ISSN: 0097-8485


  21 in total

1.  Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER.

Authors:  Gautam Aggarwal; Ramakrishna Ramaswamy
Journal:  J Biosci       Date:  2002-02       Impact factor: 1.826

Review 2.  Computational gene finding in plants.

Authors:  Mihaela Pertea; Steven L Salzberg
Journal:  Plant Mol Biol       Date:  2002-01       Impact factor: 4.076

3.  Evaluation of gene-finding programs on mammalian sequences.

Authors:  S Rogic; A K Mackworth; F B Ouellette
Journal:  Genome Res       Date:  2001-05       Impact factor: 9.043

4.  Dictionary-driven prokaryotic gene finding.

Authors:  Tetsuo Shibuya; Isidore Rigoutsos
Journal:  Nucleic Acids Res       Date:  2002-06-15       Impact factor: 16.971

Review 5.  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

6.  Gene prediction by spectral rotation measure: a new method for identifying protein-coding regions.

Authors:  Daniel Kotlar; Yizhar Lavner
Journal:  Genome Res       Date:  2003-07-17       Impact factor: 9.043

7.  Human-mouse gene identification by comparative evidence integration and evolutionary analysis.

Authors:  Lingang Zhang; Vladimir Pavlovic; Charles R Cantor; Simon Kasif
Journal:  Genome Res       Date:  2003-05-12       Impact factor: 9.043

8.  Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations.

Authors:  Poonam Singhal; B Jayaram; Surjit B Dixit; David L Beveridge
Journal:  Biophys J       Date:  2008-03-07       Impact factor: 4.033

9.  Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.

Authors:  Vladimir Paar; Nenad Pavin; Ivan Basar; Marija Rosandić; Matko Gluncić; Nils Paar
Journal:  BMC Bioinformatics       Date:  2008-11-03       Impact factor: 3.169

10.  Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation.

Authors:  Chuanhua Xing; Donald L Bitzer; Winser E Alexander; Mladen A Vouk; Anne-Marie Stomp
Journal:  Nucleic Acids Res       Date:  2008-12-10       Impact factor: 16.971

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