Question: Extract single transcript sequences from genome assembly
0
gravatar for kaz0816
7 weeks ago by
kaz08160
kaz08160 wrote:

Hi,

I want to extract one transcript per gene from the genome assembly and its GFF3 file registered in Refseq. And I want to extract a transcript that has a longest or a certain frame. Anyone know of an efficient method?

I am looking for this method to do ortholog comparisons.

Best regards,

assembly genome • 135 views
ADD COMMENTlink written 7 weeks ago by kaz08160

Python and biopython can help you on that

https://biopython.org/wiki/GFF_Parsing

https://pypi.org/project/gff3/

https://pythonhosted.org/gffutils/

ADD REPLYlink written 7 weeks ago by Bastien Hervé4.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1041 users visited in the last hour