On 07/10/2011 16:27, Mahmut Uludag wrote:
> On Thu, 2011-10-06 at 19:22 -0400, PIRA (Preethi Ramaiya) wrote:
>> Is there a way to convert multiple GFF3 files into EMBL format with
>> the correct “join”  for euk. CDSes? Artemis is able to correctly read
>> and write the GFF3 /EMBL file I have but how do I do this for multiple
>> contig files. Bioperlish options seem straightforward for a one exon
>> ->one CDS mode. I have Parent and ID tags in gene/transcript/CDS
>> structure
> These were the areas Peter was working on recently, a few weeks ago.
> EMBOSS with latest patches might do the transformation but Peter should
> know the answer.

An interesting question - do these GFF3 files share identifiers? I assume these are joins across entries (e.g. CDSs that span contigs)

As Mahmut says, I made some changes recently to make EMBOSS more compatible with the GFF3 standard. Some are in the latest patches, others will be in the next release at the end of the year.

EMBOSS reads a single feature file for each sequence, but writing an application to read a set of files for one sequence is easy in principle.

For example, we could use it to combine the results of several EMBOSS applications (any motif finding application in EMBOSS can write GFF3 or other feature format output which we can read back in)


Peter Rice

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