User talk:Darek Kedra/sandbox 26

GFF Comparison

Perl scripts collection

link: http://biowiki.org/GffTools/

Tested: gffsort.pl (sorts GFF streams by sequence name and startpoint)

Python efforts

• Brad Chapman's GFF parser:

https://github.com/chapmanb/bcbb/tree/master/gff

• GFFutils by Ryan Dale:

https://github.com/daler/GFFutils

• Pygr

main link: http://code.google.com/p/pygr/

discussion about gff/annotation parsing: http://www.mail-archive.com/pygr-dev@googlegroups.com/msg01551.html

• bpbio

http://code.google.com/p/bpbio/

• bx-python

http://bitbucket.org/james_taylor/bx-python/overview

Ruby

• BioRuby library:

http://www.bioruby.org/rdoc/classes/Bio/GFF/GFF3.html

Java

Biojava module: http://www.biojava.org/docs/api/org/biojava/bio/program/gff/GFFTools.html

Stand alone programs

• Eval

link: http://mblab.wustl.edu/software/eval/ version: 2.2.8

Perl program with GUI.

• GPFE

GFPE: gene-finding program evaluation Bioinformatics (2003) 19 (13): 1712-1713. doi: 10.1093/bioinformatics/btg216

link: ftp://anonymous@iubio.bio.indiana.edu/molbio/genefind/ Program in java.

• overlap

link: http://big.crg.cat/services/overlap author: Sarah Djebali