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Current methods of gene prediction, their strengths and weaknesses

(2002) NUCLEIC ACIDS RESEARCH. 30(19). p.4103-4117
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Abstract
While the genomes of many organisms have been sequenced over the last few years, transforming such raw sequence data into knowledge remains a hard task. A great number of prediction programs have been developed that try to address one part of this problem, which consists of locating the genes along a genome. This paper reviews the existing approaches to predicting genes in eukaryotic genomes and underlines their intrinsic advantages and limitations. The main mathematical models and computational algorithms adopted are also briefly described and the resulting software classified according to both the method and the type of evidence used. Finally, the several difficulties and pitfalls encountered by the programs are detailed, showing that improvements are needed and that new directions must be considered.
Keywords
BACTERIAL GENOME, ISOCHORE ORGANIZATION, EUKARYOTIC DNA, FINDING GENES, ARABIDOPSIS-THALIANA, GENOMIC DNA-SEQUENCES, SPLICE-SITE PREDICTION, INTERPOLATED MARKOV-MODELS, PROTEIN-CODING REGIONS, PRE-MESSENGER-RNA

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MLA
Mathé, Catherine, Marie-France Sagot, Thomas Schiex, et al. “Current Methods of Gene Prediction, Their Strengths and Weaknesses.” NUCLEIC ACIDS RESEARCH 30.19 (2002): 4103–4117. Print.
APA
Mathé, C., Sagot, M.-F., Schiex, T., & Rouzé, P. (2002). Current methods of gene prediction, their strengths and weaknesses. NUCLEIC ACIDS RESEARCH, 30(19), 4103–4117.
Chicago author-date
Mathé, Catherine, Marie-France Sagot, Thomas Schiex, and Pierre Rouzé. 2002. “Current Methods of Gene Prediction, Their Strengths and Weaknesses.” Nucleic Acids Research 30 (19): 4103–4117.
Chicago author-date (all authors)
Mathé, Catherine, Marie-France Sagot, Thomas Schiex, and Pierre Rouzé. 2002. “Current Methods of Gene Prediction, Their Strengths and Weaknesses.” Nucleic Acids Research 30 (19): 4103–4117.
Vancouver
1.
Mathé C, Sagot M-F, Schiex T, Rouzé P. Current methods of gene prediction, their strengths and weaknesses. NUCLEIC ACIDS RESEARCH. 2002;30(19):4103–17.
IEEE
[1]
C. Mathé, M.-F. Sagot, T. Schiex, and P. Rouzé, “Current methods of gene prediction, their strengths and weaknesses,” NUCLEIC ACIDS RESEARCH, vol. 30, no. 19, pp. 4103–4117, 2002.
@article{153964,
  abstract     = {While the genomes of many organisms have been sequenced over the last few years, transforming such raw sequence data into knowledge remains a hard task. A great number of prediction programs have been developed that try to address one part of this problem, which consists of locating the genes along a genome. This paper reviews the existing approaches to predicting genes in eukaryotic genomes and underlines their intrinsic advantages and limitations. The main mathematical models and computational algorithms adopted are also briefly described and the resulting software classified according to both the method and the type of evidence used. Finally, the several difficulties and pitfalls encountered by the programs are detailed, showing that improvements are needed and that new directions must be considered.},
  author       = {Mathé, Catherine and Sagot, Marie-France and Schiex, Thomas and Rouzé, Pierre},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keywords     = {BACTERIAL GENOME,ISOCHORE ORGANIZATION,EUKARYOTIC DNA,FINDING GENES,ARABIDOPSIS-THALIANA,GENOMIC DNA-SEQUENCES,SPLICE-SITE PREDICTION,INTERPOLATED MARKOV-MODELS,PROTEIN-CODING REGIONS,PRE-MESSENGER-RNA},
  language     = {eng},
  number       = {19},
  pages        = {4103--4117},
  title        = {Current methods of gene prediction, their strengths and weaknesses},
  url          = {http://dx.doi.org/10.1093/nar/gkf543},
  volume       = {30},
  year         = {2002},
}

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