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Old 12-02-2012, 08:02 AM   #4
gsgs
Senior Member
 
Location: germany

Join Date: Oct 2009
Posts: 140
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well, I'm the new one since I don't know about the normal software and databases and companies etc.
I write my own software, mainly just for influenza.

After some years (!) I noticed, that for most comparisons we don't need
alignment, we can just count the number of matching subsequences of certain length, no matter at what position they appear.

I think this is also basically used in "blast", why it's so fast for big databases.

So I wrote a program for that, (Windows 32-bit,cmd.exe commandline - DOS)
but presumably there are other programs available for UNIX,Win64, etc,

I can send my program, with source code or I run your data through it
(all genbank viruses) it finds matching subsequences length 15-28

(I speculate this is what you want, but am not sure)
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