Phat -: a gene finding program for Plasmodium falciparum

被引：31

作者：

Cawley, SE ^{[1
]}

Wirth, AI

Speed, TP

机构：

[1] Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA

[2] Affymetrix, Emeryville, CA 94608 USA

[3] Princeton Univ, Dept Comp Sci, Princeton, NJ 08544 USA

来源：

MOLECULAR AND BIOCHEMICAL PARASITOLOGY | 2001年 / 118卷 / 02期

关键词：

Plasmodium falciparum; gene-finding; generalized hidden Markov model; viterbi algorithm;

D O I：

10.1016/S0166-6851(01)00363-2

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We describe and assess the performance of the gene finding program pretty handy annotation tool (Phat) on sequence from the malaria parasite Plasmodium falciparum. Phat is based on a generalized hidden Markov model (GHMM) similar to the models used in GENSCAN, Genie and HMMgcne. In a test set of 44 confirmed gene structures Phat achieves nucleotide-level sensitivity and specificity of greater than 95%, performing as well as the other P. falciparum gene finding programs Hexamer and GlimmerM. Phat is particularly useful for P. falciparum and other eukaryotes for which there are few gene finding programs available as it is distributed with code for retraining it on new organisms. Moreover, the full source code is freely available under the GNU General Public License, allowing for users to further develop and customize it. (C) 2001 Elsevier Science B.V. All rights reserved.

引用

页码：167 / 174

页数：8

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