Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.
Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.
复制标题
DOI：
10.1186/gb-2006-7-3-r24
复制
发表时间：
2006
期刊：
影响因子：
12.3
通讯作者：
Vernick KD
中科院分区：
文献类型：
--
作者：
Li J;Riehle MM;Zhang Y;Xu J;Oduol F;Gomez SM;Eiglmeier K;Ueberheide BM;Shabanowitz J;Hunt DF;Ribeiro JM;Vernick KD
冈比亚按蚊基因组的比较和从头算基因预测算法相结合的全面重新注释，确定了新的编码序列。全基因组注释是冈比亚按蚊研究人员探索这种有效疟疾载体生物学的必要工具。我们重新注释了A.冈比亚的基因组通过合成比较和从头预测的编码序列（CDS）集成一个单一的集合，使用外显子基因联盟算法，然后由开放阅读框选择算法。重新注释预测了20，970个至少有两条证据支持的CDS，并且将缺少起始和/或终止密码子的CDS的比例降低到仅约4%。重新注释的CDS集包括一组4，681个未在Ensembl注释中表示但具有EST支持的新CDS，以及另一组4，031个Ensembl支持的基因，这些基因在重新注释的集中经历了主要的结构变化，因此可能是功能变化。通过与来自20，249个全长cDNA克隆的末端序列进行比较，并评估来自A. gambiae鸟枪法蛋白质组学数据集证实了重新注释的CDS为蛋白质组学提供了高质量的蛋白质数据库。我们提供了一个功能蛋白质组学注释，ReAnoXcel，通过AnoXcel管道分析新的CDS获得，它允许在同一个生物信息学平台内对CDS集进行功能比较。CDS数据可供下载。综合A.冈比亚基因组重新注释是通过比较和从头基因预测算法的组合来实现的。
A comprehensive reannotation of the Anopheles gambiae genome using a combination of comparative and ab initio gene prediction algorithms has identified novel coding sequences. Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector. We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download. Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms.
登录
查看更多内容
影响因子：
7
作者：
Reese, MG;Hartzell, G;Lewis, SE
通讯作者：
Lewis, SE
影响因子：
4.4
作者：
Dana AN;Hong YS;Kern MK;Hillenmeyer ME;Harker BW;Lobo NF;Hogan JR;Romans P;Collins FH
通讯作者：
Collins FH
影响因子：
7
作者：
Curwen, V;Eyras, E;Clamp, M
通讯作者：
Clamp, M
影响因子：
7.4
作者：
MacCoss, MJ;Wu, CC;Yates, JR
通讯作者：
Yates, JR
影响因子：
7
作者：
Guigó, R;Agarwal, P;Fickett, JW
通讯作者：
Fickett, JW