I have the DNA coding sequence to my intrest protein, but I want to get at least 50 nucleotides up and downstream. Is there any website or program to get that?
Usually the easiest way to do it is through a genome browser supposing that your target genome has been uploaded in one of these browsers. For example, Adi3 gene (AvrPto-dependent Pto-interacting protein 3) from tomato is located in the chromosome 1 between 75673551 and 75676502. In GBrowse this region is represented as SL2.40ch01:75673551..75676502, so modifying these values in the Landmark or Region box you can target a different region. Let suppose that it is +50 dowstream, so the new region will be in the position 75673551 - 50 = 75673501 and 75673551 (SL2.40ch01:75673501..75673551). To download the sequence you can use the link at File > Export as ... > ... FASTA sequence file.
(Link: http://solgenomics.net/gbrowse/bin/gbrowse/ITAG2.3_genomic/?name=SL2.40ch01%3A75673551..75676502&h_feat=adi3).
I hope this helps,
For what species? In plants, for instance, Phytozome (http://www.phytozome.net/) allows to search for particular genes within a species giving information about gene structure and predicted protein domains. Once in the specific gene page, under the section "sequences" you can get the genomic region containing your gene of interest and choose different values for additional upstream and downstream nucleotides (I use that for getting promoter regions). I'm pretty sure other databases have similar tools.
Good luck!
You could start at NCBI.
http://www.ncbi.nlm.nih.gov/gene/11475 (for actin gene)
if it is for only one gene, then I would suggest you to go manually by NCBI blast (grab its location) followed by extracting the +-50bp by NCBI itself [see the side pane for "Change region shown"].
Thank you so much all of you for kindly assistance. I appreciate your time.
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