Coverting Embl Format To Bed Format

Question

[bioinfo]

I have an embl file of my annotated genome. How can I convert it to bed format so I can use it in Bed tools? Will I get the output like that in the converted bed file from embl? e.g.

Gene     start      end 
BRCA      120       279
BRCB      390       578
CDRA      890       1176

Answer 1

[Istvan Albert]

Try ReadSeq http://www.ebi.ac.uk/cgi-bin/readseq.cgi

EDIT:

indeed ReadSeq does not convert to BED. Well then just convert to GFF then convert that to BED, see this perhaps

http://www.biostars.org/post/show/2/how-do-i-convert-from-bed-format-to-gff-format/

[bioinfo]

had a look before but there is no option to convert in Bed format

[Istvan Albert]

I guess you would need to convert GFF to BED then. Ah ... I just remembered that converting BED to GFF was the first question that I posted on Biostar: http://www.biostars.org/post/show/2/how-do-i-convert-from-bed-format-to-gff-format/

[bioinfo]

thanks..I am going through it

[bioinfo]

I managed to convert my embl format to C++ text format..now I m trying to convert that to bed