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Extract gene sequences from gff3 file and reference fasta

Hi,

I have a gff3 file and I want to extract the gene sequences (not including introns). Several genes have many isoforms, but I want only the gene sequence (i.e. all the exons spliced). Anyone know of a tool that does this? I tried gffread from the tophat package but I could not get only the gene sequence.

Sample of my gff3 file:

##gff-version 3
###
scis2053        noncoding       gene    27485   28677   .       -       .       ID=scign013105;Name=scign013105
scis2053        noncoding       mRNA    27485   28677   5921    -       .       ID=scitn013105.1;Parent=scign013105;Name=scitn013105.1
scis2053        noncoding       exon    27485   28677   .       -       .       Parent=scitn013105.1
###
scis673 noncoding       gene    85677   115116  .       +       .       ID=scign002358;Name=scign002358
scis673 noncoding       mRNA    113016  115116  6254    +       .       ID=scitn002358.1;Parent=scign002358;Name=scitn002358.1
scis673 noncoding       exon    113016  113049  .       +       .       Parent=scitn002358.1
scis673 noncoding       exon    113444  114538  .       +       .       Parent=scitn002358.1
scis673 noncoding       exon    114973  115116  .       +       .       Parent=scitn002358.1
scis673 noncoding       mRNA    85677   115099  3835    +       .       ID=scitn002358.2;Parent=scign002358;Name=scitn002358.2
scis673 noncoding       exon    85677   85697   .       +       .       Parent=scitn002358.2
scis673 noncoding       exon    113896  114538  .       +       .       Parent=scitn002358.2
scis673 noncoding       exon    114973  115099  .       +       .       Parent=scitn002358.2
gff3 fasta
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written by jon.brate jon.brate

1 answer

Hello jon.brate!

It feels like this must have been asked virtually 100 times, but this question should provide a working BioPerl answer. In the example given the cdna file should be what you are asking for.

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

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written by Michael Dondrup Michael Dondrup

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