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

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 clo...

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Published in:Bioinformatics 2004-12, Vol.20 (18), p.3676-3679
Main Authors: Gisel, Andreas, Panetta, Maria, Grillo, Giorgio, Licciulli, Vito Flavio, Liuni, Sabino, Saccone, Cecilia, Pesole, Graziano
Format: Article
Language:English
Subjects:
Algorithms
Artificial Intelligence
Biological and medical sciences
Conserved Sequence
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Pattern Recognition, Automated - methods
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Sequence Homology, Nucleic Acid
Software
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container_end_page 3679
container_issue 18
container_start_page 3676
container_title Bioinformatics
container_volume 20
creator Gisel, Andreas
Panetta, Maria
Grillo, Giorgio
Licciulli, Vito Flavio
Liuni, Sabino
Saccone, Cecilia
Pesole, Graziano
description 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. Availability: http://bighost.ba.itb.cnr.it:8080/Framework
doi_str_mv 10.1093/bioinformatics/bth420
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source Oxford University Press Open Access
subjects Algorithms
Artificial Intelligence
Biological and medical sciences
Conserved Sequence
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Pattern Recognition, Automated - methods
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Sequence Homology, Nucleic Acid
Software
title DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions
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