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How to generate GTF file from BLAST output?

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
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written by mathavanbioinfo mathavanbioinfo

A GTF file of what?

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

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written by lieven.sterck lieven.sterck

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.

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written by GenoMax GenoMax

2 answers

The Ensembl GTFs contain the mitochondrial genes.

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written by Emily Emily

Mam I working on Bubalus bubalis (water buffalo)

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written by mathavanbioinfo mathavanbioinfo

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.

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written by i.sudbery i.sudbery

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