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Old 06-02-2012, 09:22 AM   #1
paula123
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Default entamoeba histolytica reference genome (gene annotation file) in GTF format

Hi,
I am working with Entamoeba data. I have downloaded the genome data of entamoeba from NCBI in genebank format but did not get in GTF format. I have searched it in UCSC genome browser but unable to find out. Can any one suggest me in either find out it in GTF format or converting from genebank t GTF format ?
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Old 06-04-2012, 02:39 AM   #2
arvid
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If you are able to do a bit of Python coding on your own you could use the bcbio BioPython module for GFF parsing/writing from the following page; there is a description on how to convert GenBank flat format annotation files into GFF3:
http://biopython.org/wiki/GFF_Parsing#Writing_GFF3

Then you could use the GenomeTools (http://genometools.org/) gff3_to_gtf tool to get proper GTF (if necessary, many tools can use GFF3 as well).
I've done this before though I've seen troubles with certain GenBank files, as some features are difficult to correctly translate into GFF3. You might need to manually check that the contents are correct, or filter out stuff that isn't needed in the end, to avoid problems with the GenomeTools converter.
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