Question

How to generate GTF file from BLAST output?

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2.9 years ago

mathavanbioinfo ▴ 90

Hello All, How to create a GTF file, I have only sequence level of information available (fasta format)

Note: I am working on mitochondrial genome, no GTF file available in any repository

Regards Mathavan M

GTF • 1.7k views

ADD COMMENT • link 2.9 years ago by mathavanbioinfo ▴ 90

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A GTF file of what?

In general you question is lacking some crucial bits of information to get meaningful answers/support here.

ADD REPLY • link 2.9 years ago by lieven.sterck 15k

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I am working on bovine genome

ADD REPLY • link 2.9 years ago by mathavanbioinfo ▴ 90

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Since the title of the question refers to converting a BLAST output to GTF here is one representative tool (LINK). You will need to see if it works for your purpose. There are others but YMMV.

ADD REPLY • link 2.9 years ago by GenoMax 141k

score 3 · Answer 1 · 2021-06-15

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2.9 years ago

Emily 23k

The Ensembl GTFs contain the mitochondrial genes.

ADD COMMENT • link 2.9 years ago by Emily 23k

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Mam I working on Bubalus bubalis (water buffalo)

ADD REPLY • link 2.9 years ago by mathavanbioinfo ▴ 90

score 3 · Answer 2 · 2021-06-15

I don't think this is what the OP wants, but to answer the actual question:

Probably the easiest way to get BLAST output as a GTF file is to use commandline BLAST, and to set the outfmt to 17 (SAM), and then convert the SAM output to gff. And the easiest way to do that might be sam2bed and then bed2gff from bedops.