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


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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1471 users visited in the last hour