在果蝇注释实验中使用GeneWise。
Using GeneWise in the Drosophila annotation experiment.
作者信息
Birney E, Durbin R
机构信息
Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
出版信息
Genome Res. 2000 Apr;10(4):547-8. doi: 10.1101/gr.10.4.547.
Abstract
The GeneWise method for combining gene prediction and homology searches was applied to the 2.9-Mb region from Drosophila melanogaster. The results from the Genome Annotation Assessment Project (GASP) showed that GeneWise provided reasonably accurate gene predictions. Further investigation indicates that many of the incorrect gene predictions from GeneWise were due to transposons with valid protein-coding genes and the remaining cases are pseudogenes or possible annotation oversights.
摘要
用于结合基因预测和同源性搜索的GeneWise方法被应用于黑腹果蝇的2.9兆碱基区域。基因组注释评估项目（GASP）的结果表明，GeneWise提供了相当准确的基因预测。进一步的研究表明，GeneWise中许多错误的基因预测是由于带有有效蛋白质编码基因的转座子，其余情况是假基因或可能的注释疏忽。
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本文引用的文献
1
Drosophila genomic sequence annotation using the BLOCKS+ database.使用BLOCKS+数据库对果蝇基因组序列进行注释。
Genome Res. 2000 Apr;10(4):543-6. doi: 10.1101/gr.10.4.543.
2
Genome annotation assessment in Drosophila melanogaster.黑腹果蝇的基因组注释评估
Genome Res. 2000 Apr;10(4):483-501. doi: 10.1101/gr.10.4.483.
3
The Pfam protein families database.Pfam蛋白质家族数据库。
Nucleic Acids Res. 2000 Jan 1;28(1):263-6. doi: 10.1093/nar/28.1.263.
4
Critical assessment of methods of protein structure prediction (CASP): round III.蛋白质结构预测方法的批判性评估（CASP）：第三轮。
Proteins. 1999;Suppl 3:2-6.
5
Profile hidden Markov models.轮廓隐马尔可夫模型
Bioinformatics. 1998;14(9):755-63. doi: 10.1093/bioinformatics/14.9.755.
6
Two methods for improving performance of an HMM and their application for gene finding.两种提高隐马尔可夫模型性能的方法及其在基因识别中的应用。
Proc Int Conf Intell Syst Mol Biol. 1997;5:179-86.
7
Prediction of complete gene structures in human genomic DNA.人类基因组DNA中完整基因结构的预测。
J Mol Biol. 1997 Apr 25;268(1):78-94. doi: 10.1006/jmbi.1997.0951.
8
A generalized hidden Markov model for the recognition of human genes in DNA.一种用于识别DNA中人类基因的广义隐马尔可夫模型。
Proc Int Conf Intell Syst Mol Biol. 1996;4:134-42.
9
Discovering and understanding genes in human DNA sequence using GRAIL.使用GRAIL在人类DNA序列中发现并理解基因。
Methods Enzymol. 1996;266:259-81. doi: 10.1016/s0076-6879(96)66018-2.
10
Hidden Markov models in computational biology. Applications to protein modeling.计算生物学中的隐马尔可夫模型。在蛋白质建模中的应用。
J Mol Biol. 1994 Feb 4;235(5):1501-31. doi: 10.1006/jmbi.1994.1104.
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