Question: A Map(?) Of Sequence Alignment
gravatar for Karol Pal jr.
6.2 years ago by
Czech Republic
Karol Pal jr.20 wrote:


I'm finding it hard to express my problem in very few words (so I may have missed the solution to my problem while googling for it). I need to align two sequences, but as an output I want to know which base of my sequence translates to which base of the reference sequence, so I would get a sort of a map. I don't need to see two lines of letters under each other.

To explain, I want to use this map as a part of my code, to bridge some information about the sequence at the input side and some at the reference side (SNP's). I have a hunch this kind of mapping is used somewhere along while doing a classical alignment, but I wouldn't mind your advice before I start digging in the code of aligners.

Nevertheless I still need to keep this alignment 'classical' in the sense to know where the gaps and variations are.

Thanks for any hints/suggestions.

sequence aligner alignment • 1.3k views
ADD COMMENTlink modified 6.2 years ago by zam.iqbal.genome1.7k • written 6.2 years ago by Karol Pal jr.20

Not sure that this is what you are looking for, but look into biopython, slice alignments. (

ADD REPLYlink written 6.2 years ago by Whetting1.5k

Do you look for something like a .vcf file? It includes the variants of a sequence in reference to another. (

ADD REPLYlink written 6.2 years ago by skymningen330
gravatar for zam.iqbal.genome
6.2 years ago by
United Kingdom
zam.iqbal.genome1.7k wrote:

You are just asking for a mapping between coordinates in the two strings? eg for



is your map (in the mathematical sense)






where left hand number is coordinate in AACGT and right-hand is coordinate in ACTT? How do you want to define the value which it assigns to 3? Sounds like you could write something very easily which takes output from a standard aligner?

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by zam.iqbal.genome1.7k

Yes this is exactly how I imagined it. Assigning the left 3 something like 2.1 on the right. An yes, I too believe it shouldn't be complicated to write something like that, but it seems to me like doing unnecessary backtracking (since I assume a map like this would be built in a program during the process of alignment, my idea was to exploit this map - if there is one like that and I could get access to it through the code).

ADD REPLYlink written 6.2 years ago by Karol Pal jr.20
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: 1561 users visited in the last hour