BMC Research Notes | |
GFF-Ex: a genome feature extraction package | |
Dinesh Gupta1  Achal Rastogi1  | |
[1] Bioinformatics Laboratory, Structural and Computational Biology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India | |
关键词: Sequence parser; Annotation; Genomics; GFF; | |
Others : 1132697 DOI : 10.1186/1756-0500-7-315 |
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received in 2013-02-01, accepted in 2014-03-21, 发布年份 2014 | |
【 摘 要 】
Background
Genomic features of whole genome sequences emerging from various sequencing and annotation projects are represented and stored in several formats. Amongst these formats, the GFF (Generic/General Feature Format) has emerged as a widely accepted, portable and successfully used flat file format for genome annotation storage. With an increasing interest in genome annotation projects and secondary and meta-analysis, there is a need for efficient tools to extract sequences of interests from GFF files.
Findings
We have developed GFF-Ex to automate feature-based extraction of sequences from a GFF file. In addition to automated sequence extraction of the features described within a feature file, GFF-Ex also assigns boundaries for the features (introns, intergenic, regions upstream to genes), which are not explicitly specified in the GFF format, and exports the corresponding primary sequence information into predefined feature specific output files. GFF-Ex package consists of several UNIX Shell and PERL scripts.
Conclusions
Compared to other available GFF parsers, GFF-Ex is a simpler tool, which permits sequence retrieval based on additional inferred features. GFF-Ex can also be integrated with any genome annotation or analysis pipeline. GFF-Ex is freely available at http://bioinfo.icgeb.res.in/gff webcite.
【 授权许可】
2014 Rastogi and Gupta; licensee BioMed Central Ltd.
【 预 览 】
Files | Size | Format | View |
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20150304045442765.pdf | 626KB | download | |
Figure 1. | 96KB | Image | download |
【 图 表 】
Figure 1.
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