Q on

clwu newgene at bigfoot.com
Wed Jan 15 18:38:07 UTC 2003

Thank you, Stefanie. I can get the different sequences I needed by 
parsing the global alignment result. But I think if diffseq can be 
implemented to use both local and global alignment to give the all 
different sequences directly, that will make it do the job as its name.

Just a suggestion.


Stefanie Lager wrote:

>diffseq use a local wordmatch alignment algorithm, it finds gaps but
>at the ends you can't match against NOTHING. Try using a global
>alignment algorithm instead (e.g. needle or stretcher). But maybe it
>could be an option in diffseq to use either use a local or global
>alignment algorithm?
>>Hi, Group,
>>I have one copy of EMBOSS (ver2.5.1) installed locally under
>>cygwin/win2k. I expected "diffseq" can do the job as its name.
>>However, I found it can not identify the different sequence at the
>>both ends of input sequences. Only the different seq. inside can
>>be indentified. Why? Is it the design purpose? How can I get all
>>different sequences I need?
>>Thank you.
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