do we need alignment ?

[gsgs]

I recently discovered to compare sequences by their matching subsequences
- say - of length 12 for nucleotides.
This has the advantage that you needn't align the sequences,
which may take quite some time (usinf MAFFT) for large sets
and can't be done from batch.
You can also store many subsequences in an array and quickly scan
whole databases for matches

Now I wonder how good/reliable that method is to measure
genetic similarity ? Is it generally being done to replace alignment ?

I'm mainly doing it for influenza

[krobison]

Whether you need any analysis is defined by what question you are asking. Since you haven't stated a hypothesis, it's rather challenging to answer whether a given approach would answer that hypothesis.

In any case, many sequence database search tools employ some variant on what you are describing. The Burrows-Wheeler transform that lies at the heart of Bowtie, BWA and many other short read aligners is a scheme for efficiently searching a very large table of subsequences -- simply storing subsequences in an array breaks down very quickly.

[gsgs]

multiple purposes. Currently I was trying to compute the distance-graph
(<x% nucleotide-differences ?) and then trying to find a small dominating
set, such than any other sequence is closer than (100-x)% to one
in the dominating set. Hopefully easier to handle than the big databases
while it still contains essentially all sequences.

Other applications/problems/questions: search for recombinations,
reassortments,
for periods of low mutation (graph: differences vs. time-difference)
or nucleotide vs. amino acid mutations

track mutations, where they appear first,
mutation pictures


for many of the purposes, i.e. the distance graph maybe the
alignment isn't needed ? But I'm not sure how "good" the
subsequence-distances are

-----------------------------------------
2012/06/04

the pic below shows that it is a bit less sensitive,
but acceptable

avian influenza segment1 pairs
amino-acid differences vs. nucleotide-differences