GFF-Ex: a genome feature extraction package

BMC Research Notes

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

 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.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]Metzker ML: Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31-46.
• [2]Marguerat S, Bahler J: RNA-seq: from technology to biology. Cell Mol Life Sci 2010, 67(4):569-579.
• [3]Kawaji H, Hayashizaki Y: Genome annotation. Methods Mol Biol 2008, 452:125-139.
• [4]Pruitt KD, Tatusova T, Klimke W, Maglott DR: NCBI reference sequences: current status, policy and new initiatives. Nucleic Acids Res 2009, 37(Database issue):D32-36.
• [5]Kyrpides NC: Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat Biotechnol 2009, 27(7):627-632.
• [6]Eilbeck K, Moore B, Holt C, Yandell M: Quantitative measures for the management and comparison of annotated genomes. BMC Bioinforma 2009, 10:67. BioMed Central Full Text
• [7]Chatterji S, Pachter L: Reference based annotation with GeneMapper. Genome Biol 2006, 7(4):R29. BioMed Central Full Text
• [8]Sangers Institute GFF Perl Modules http://www.sanger.ac.uk/resources/software/gff/#t_1 webcite
• [9]Josep Abril’s GFF programs http://www.sanger.ac.uk/resources/software/gff/#t_2 webcite
• [10]BioPerl http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Tools/GFF.pm webcite
• [11]Cufflinks 2.0.0 http://cufflinks.cbcb.umd.edu/gff.html webcite
• [12]Galaxy Server: Extract Genomic DNA ver2.2.2 http://galaxy.raetschlab.org/root?tool_id=Extract_features1 webcite