standard file format to specify where exons are

Question

[Jorge Maturana]

Hello All,

I'm a newbie in bioinformatics, so I apologyze for my -maybe- basic question.

I'm working on a software to create primer panel to perform PCR for the exome of a gene. My idea is to give my program a file with a declaration of the gene and its structure (exons, UTRs).

I know that a FASTA/FASTQ file can hold the DNA string of the gene, but I haven't found a way to tell the program where each exon/UTR starts and ends. I could create my own file format, but I imagine that there's a standard one, so I can download the structure form an online repository and sending to my program without edition.

Since I want to include some intronic bases before and after the exon, a FASTA/Q file with just exons is not useful for me.

I would appreciate any clue that you can give me!

Thanks in advance,

Jorge

Answer 1

[Pierre Lindenbaum]

GTF format: https://en.wikipedia.org/wiki/Gene_transfer_format

UCSC BED format: https://genome.ucsc.edu/FAQ/FAQformat.html#format1 (see columns 10,11,12) for exons and 7,8 for CDS.

[Jorge Maturana]

Merci Pierre !

[Ram]

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Answer 2

[Ram]

Take a look at the GTF format.