Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing

被引：16

作者：

Walenz, Brian ^{[2
]}

Florea, Liliana ^{[1
]}

机构：

[1] Univ Maryland, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA

[2] J Craig Venter Inst, Rockville, MD 20850 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 13期

基金：

美国国家卫生研究院;

关键词：

PROGRAM;

D O I：

10.1093/bioinformatics/btr285

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The large number of genomes that will be sequenced will need to be annotated with genes and other functional features. Aligning gene sequences from a related species to the target genome is an economical and highly reliable method to identify genes; unfortunately, existing tools have been lacking in sensitivity and speed. A program we reported, sim4cc, was shown to be highly accurate but is limited to comparing one cDNA with one genomic sequence. We present here an optimization of the tool, implemented in the packages sim4db and leaff. The new tool performs batch alignments of cDNA and genomic sequences in a fraction of the time required by its predecessor, and thus is very well suited for genome-wide analyses.

引用

页码：1869 / 1870

页数：2

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