Question: Appropriate Alignment Algorithm
0
gravatar for Maria
5.3 years ago by
Maria150
Maria150 wrote:

Hi, I want to compare 2 genomic sequences, one is the reference (r) the other is the query, the reference is composed of 2 genes (mitochondria 16kbp each) and the intergenic seq in between, the other is the (q1) sequence which is the left gene in other species (homologous) with the next intergenic sequence in this this species, and another alignment is between the reference (r) and the homologous right gene with the intergenic sequence in this species 2 alignments Note that the 2 genes could be not consecutive in the query specie i.e. if X and Y are two genes and --- is the non coding sequence in between we have X---Y in reference but X---Z---Y in the other species.

I aim at studiying the region between the 2 vertical lines in the picture, what is the best alignment approach to do it ? i.e global/local/semi global/mixte? and what about the alignment parameters i.e match mismatch and gap penalty ?

alignment • 1.9k views
ADD COMMENTlink modified 5.3 years ago by rob234king560 • written 5.3 years ago by Maria150
1

FYI, I modified your post such that the image displays. Sorry and please let me know if I did that in error.

ADD REPLYlink written 5.3 years ago by Devon Ryan88k
1
gravatar for hpaces
5.3 years ago by
hpaces10
hpaces10 wrote:

try mummer http://mummer.sourceforge.net/

ADD COMMENTlink written 5.3 years ago by hpaces10
1
gravatar for rob234king
5.3 years ago by
rob234king560
UK/Harpenden/Rothamsted Research
rob234king560 wrote:

If you have geneious at work (work has to pay for it) then can use multiple alignment option or other sequence comparison tools, or the free mummer as above is commonly used.

ADD COMMENTlink written 5.3 years ago by rob234king560

my question is about the choice of parameters, and alignment type

ADD REPLYlink written 5.3 years ago by Maria150

my question is about the choice of parameters, and alignment type

ADD REPLYlink written 5.3 years ago by Maria150
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