Question: Counting the number of Guanine bases between certain points in a sequence (FASTA file)
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gravatar for shedges.49
13 days ago by
shedges.490
shedges.490 wrote:

Hi,

I have been tackling with this for quite some time now and I think it is time for me to ask for help...

I have multiple paired samples (e.g. ID 1a,1b,2a,2b,3a,3b,4a,4b...) and their sequences for a specific locus, e.g. Locus 1. These are contingency loci and I am interested in the hyperpolymetric tract within this sequence, e.g. --GGGGGGGG-- and this can vary between sample i.e. ID 1a(8), 1b(9). I am interested in extracting where these tracts are within the loci (I have aligned the sequences) and somehow coding or calculating how many of these bases there are in a row for each sample as I need to compare between the pairs.

I currently use MEGA to visualise my sequences, and I know that the tract starts at for example site 2660 and finishes at 2669.

I am yet to find a quick way of being able to do this, so any help would be greatly appreciated. I am also very new to bioinformatics.

ADD COMMENTlink written 13 days ago by shedges.490
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