Hello everyone,
Could someone tell me how do I download the contig where is my gene of interest?
Many thanks in advance
I think they’ve closed all the sequence gaps in the C. elegans genome, so the contig containing your gene would be a chromosome. That’s probably more than you want, though.
Your question is a bit unclear. I assume you’re asking for the sequenced genomic clone containing your gene? I find these to be useful, because it’s a manageable amount of sequence I can use to find oligos, define constructs, etcetera.
So, if this is what you want, the first thing is to identify it. If you go to the WormBase page for your gene - let’s use unc-1 as an example - then in the Overview tab you’ll see something called the “Sequence”, in this case K03E6.5. That means that the genomic clone K03E6 was sequenced, and this was the fifth gene annotated on it. So, you want K03E6.
There are a couple of places you can get this. The sequences of these genomic clones have been deposited in the NCBI, so you can start there, and do a search for K03E6. This will get you the sequence of this genomic clone, usually as the top hit, and it’s easy to switch between formats you might find convenient - FASTA, GenBank, etcetera. It will also return the sequence of the whole chromosome containing that genomic clone, if that’s the contig you want.
Or, of course, you can stay within WormBase. Back on that unc-1 gene page I linked earlier, a couple of lines below the Sequence name, there is a hyperlink to that genomic clone, and immediately below that another hyperlink to the sequence of that genomic clone, labeled “Parent seq”. Play around with these for a bit and you can find all sorts of information, annotation, and visual representation for this genomic clone. You can also find the sequence of the genomic clone (at “view sequence” on the sequence page, unsurprisingly).
also, if you are looking at the locus using the genome browser you can click/hold and drag to select a section of the genomic sequence (on the bottom calibrated line) and once you release the mouse
button a little window will pop up and you will have the option to dump the selection as fasta. choose that and then you can copy the sequence and paste into whatever local dna software you are using.
the nice thing about that option is it will give you the sequence flanking your gene of interest.
Thank you very much!
That is exactly what I nedeed! I was looking for the sequence flanking the gene of interest in order to find oligos to amplify the promotor of the gene.
Thank you again for your time!