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-   -   finding exon numbers in fasta exon file (http://seqanswers.com/forums/showthread.php?t=14921)

efoss 10-20-2011 01:57 PM

finding exon numbers in fasta exon file
 
I downloaded a file called "dmel-all-exon-r5.41.fasta.gz" from flybase.org (files -> precomputed files -> Drosophila melanogaster (Dmel) -> dmel-all-exon-r5.41.fasta.gz). The header lines for this fasta file often begin like this:

>CG3428:1 type=exon
>CG3428:2 type=exon
>CG3428:3 type=exon

I see I have exon 1, exon 2 and exon 3 for CG3428. But how am I to interpret something like this:

>CG31523:293728-293566 type=exon

The exon number is a range rather than a single number, so what does this mean?

Thank you.

Eric

efoss 10-20-2011 03:57 PM

Quote:

Originally Posted by efoss (Post 54526)
I downloaded a file called "dmel-all-exon-r5.41.fasta.gz" from flybase.org (files -> precomputed files -> Drosophila melanogaster (Dmel) -> dmel-all-exon-r5.41.fasta.gz). The header lines for this fasta file often begin like this:

>CG3428:1 type=exon
>CG3428:2 type=exon
>CG3428:3 type=exon

I see I have exon 1, exon 2 and exon 3 for CG3428. But how am I to interpret something like this:

>CG31523:293728-293566 type=exon

The exon number is a range rather than a single number, so what does this mean?

Thank you.

Eric

I think I have figured out the answer to my question - those numbers aren't exon numbers but are instead simply numbers to create unique identifiers.


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