SEQanswers - View Single Post - One read has many alignments starting at the same position

seb567 · 02-02-2011, 10:36 AM

Dear SEQanswers,

I have a particular gene. I use its sequence as a reference to gather an atlas of variations induced by some enzyme, whose target is located within the said gene sequence.

The sequence of the region of interest follows.

Code:

gatattgatattggtcttaatatgacttgttttcattgttctcaggtacctcagccagcatggcagcctctttcccacccaccttgggactca

In the sequence, two repeated 4-mers are colored in red.

I also happen to have two short reads obtained by DNA sequencing.

FORWARD:

gatattgatattggtcttaatatgacttgttttcattgttctcagccagcatggcagcctctttcccacccac

REVERSE:

tggtcttaatatgacttgttttcattgttctcagccagcatggcagcctctttcccacccaccttgggactca

Aligning these sequences onto the aforementioned reference sequence can potentially produce at least 5 alignments, regardless of utilized alignment software & algorithms.

Alignment 1

Code:

gatattgatattggtcttaatatgacttgttttcattgttctca---------gccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgttctca---------gccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgttctcaggtacctcagccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 2

Code:

gatattgatattggtcttaatatgacttgttttcattgttctc---------agccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgttctc---------agccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgttctcaggtacctcagccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 3

Code:

gatattgatattggtcttaatatgacttgttttcattgttct---------cagccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgttct---------cagccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgttctcaggtacctcagccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 4

Code:

gatattgatattggtcttaatatgacttgttttcattgttc---------tcagccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgttc---------tcagccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgttctcaggtacctcagccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 5

Code:

gatattgatattggtcttaatatgacttgttttcattgtt---------ctcagccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgtt---------ctcagccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgttctcaggtacctcagccagcatggcagcctctttcccacccaccttgggactca GENE

Alignment 6

Code:

gatattgatattggtcttaatatgacttgttttcattgt--t-------ctcagccagcatggcagcctctttcccacccac FORWARD
           tggtcttaatatgacttgttttcattgt--t-------ctcagccagcatggcagcctctttcccacccaccttgggactca REVERSE
gatattgatattggtcttaatatgacttgttttcattgttctcaggtacctcagccagcatggcagcctctttcccacccaccttgggactca GENE

(alignments omitted)

I can rule out the alignment number 6 and similar omitted alignments by considering them too complex in comparison to the 5 others.

Therefore, there is a deletion of 9 nucleotides.

However, the deletion can potentially start at 5 different positions.

Based solely on sequence information, I think there is just nothing that can be done to retrieve the true starting position of the deletion.

SEQanswers, what do you think ?

-Seb