DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions

被引：5

作者：

Gisel, A

Panetta, M

Grillo, G

Licciulli, VF

Liuni, S

Saccone, C

Pesole, G

机构：

[1] Univ Milan, Dipartimento Sci Biomol & Biotechnol, I-20133 Milan, Italy

[2] CNR, Sez Bioinformat & Genom Bari, Ist Tecnol Biomed, I-70126 Bari, Italy

[3] Univ Bari, Dipartimento Biochim & Biol Mol, I-70125 Bari, Italy

来源：

BIOINFORMATICS | 2004年 / 20卷 / 18期

关键词：

D O I：

10.1093/bioinformatics/bth420

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

DNAfan (DNA Feature ANalyzer) is a tool combining sequence-filtering and pattern searching. DNAfan automatically extracts user-defined sets of sequence fragments from large sequence sets. Fragments are defined by annotated gene feature keys and co- or non-occurring patterns within the feature or close to it. A gene feature parser and a pattern-based filter tool localizes and extracts the specific subset of sequences. The selected sequence data can subsequently be retrieved for analyses or further processed with DNAfan to find the occurrence of specific patterns or structural motifs. DNAfan is a powerful tool for pattern analysis. Its filter features restricts the pattern search to a well-defined set of sequences, allowing drastic reduction in false positive hits.

引用

页码：3676 / 3679

页数：4

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