GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.
复制标题
DOI：
10.1186/1471-2105-5-178
复制
发表时间：
2004-11-18
影响因子：
3
通讯作者：
Barton GJ
中科院分区：
文献类型：
--
作者：
Martin DM;Berriman M;Barton GJ
新基因产物的功能通常通过相似序列的注释传递分配来预测。我们描述了一种新的方法，GOtcha，预测基因产物功能的注释与基因本体论（GO）的条款。GOtcha预测GO术语与术语特定概率（P得分）置信度的关联。特定于术语的概率是GOtcha的一个新特性，允许识别注释中的冲突或不确定性。GOtcha方法应用于最近测序的恶性疟原虫基因组和其他六个基因组。定量比较GOtcha用于检索指定的GO术语与来自最高评分注释的BLAST检索命中（TOPBLAST）的直接传递分配。GOtcha将信息深入到相似性搜索匹配的“边缘地带”，利用了许多被更简单的方法丢弃的信息。在50%的P分数截止值下，GOtcha提供了比TOPBLAST在10-4的E值截止值下更好的60%的注释术语回收率和更高的20%的选择性。GOtcha方法是基因组注释者的有用工具。它已经确定了原始恶性疟原虫注释中的错误和遗漏，并被许多其他基因组测序项目所采用。
The function of a novel gene product is typically predicted by transitive assignment of annotation from similar sequences. We describe a novel method, GOtcha, for predicting gene product function by annotation with Gene Ontology (GO) terms. GOtcha predicts GO term associations with term-specific probability (P-score) measures of confidence. Term-specific probabilities are a novel feature of GOtcha and allow the identification of conflicts or uncertainty in annotation. The GOtcha method was applied to the recently sequenced genome for Plasmodium falciparum and six other genomes. GOtcha was compared quantitatively for retrieval of assigned GO terms against direct transitive assignment from the highest scoring annotated BLAST search hit (TOPBLAST). GOtcha exploits information deep into the 'twilight zone' of similarity search matches, making use of much information that is otherwise discarded by more simplistic approaches. At a P-score cutoff of 50%, GOtcha provided 60% better recovery of annotation terms and 20% higher selectivity than annotation with TOPBLAST at an E-value cutoff of 10-4. The GOtcha method is a useful tool for genome annotators. It has identified both errors and omissions in the original Plasmodium falciparum annotation and is being adopted by many other genome sequencing projects.
登录
查看更多内容
比较蛋白质组学资源：拟南芥的蛋白质。
影响因子：
12.3
作者：
Li, Wilfred W;Quinn, Greg B;Alexandrov, Nickolai N;Bourne, Philip E;Shindyalov, Ilya N
通讯作者：
Shindyalov, Ilya N
影响因子：
14.9
作者：
Huala, E;Dickerman, AW;Rhee, SY
通讯作者：
Rhee, SY
影响因子：
14.9
作者：
Stein, L;Sternberg, P;Spieth, J
通讯作者：
Spieth, J
影响因子：
7
作者：
Schug, J;Diskin, S;Stoeckert, CJ
通讯作者：
Stoeckert, CJ
影响因子：
64.8
作者：
Heidelberg JF;Eisen JA;Nelson WC;Clayton RA;Gwinn ML;Dodson RJ;Haft DH;Hickey EK;Peterson JD;Umayam L;Gill SR;Nelson KE;Read TD;Tettelin H;Richardson D;Ermolaeva MD;Vamathevan J;Bass S;Qin H;Dragoi I;Sellers P;McDonald L;Utterback T;Fleishmann RD;Nierman WC;White O;Salzberg SL;Smith HO;Colwell RR;Mekalanos JJ;Venter JC;Fraser CM
通讯作者：
Fraser CM