[BiO BB] All-vs-All Global protein seq alignment score

Dr. Christoph Gille christoph.gille at charite.de
Mon Jan 10 16:30:39 EST 2005

I have added this to the alignment program STRAP.

Load all 400 sequences into the program.

Chose from the menu analysis/ compare some sequences.

chose table and not graph and select alignment score as a distance measure.

click the hand icon to select an alignment procetdure like neobio or
clustalw or whatever. Only those that provide a score can be used.

And wait for the computation to be completed.

The output is a flat text list.

Before you analyse the 400 sequences try everything with 10 sequences.

good luck


> Hi All,
> I have a database of about 400 squences, which I want to compare
> All-vs-All to get the global alignment score of each protein sequence
> pair. I tried using bl2seq but that gives me local alignments.
> What other program would suit this function best ?
> I would probably like to have the flexibility of being able to use
> various matrices.
> Thanks a lot,
> -Manisha
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