[emboss-dev] Enquiry about emboss needleall program

Peter Rice pmr at ebi.ac.uk
Fri Jul 22 07:30:33 UTC 2011

On 22/07/2011 06:19, Tae-Kyung Kim wrote:
> Hi,
> I am now trying to perform many-to-many global sequence alignment.
> I know that *needleall* supports such a operation, but I would like to get
> the same result with a needle program including alignment, identity.
> Is there any method to get it?

Why do you want to use needle instead of needleall?

needleall reads two sets of sequences (many to many)

needle reads a single sequence, and a set of sequences to compare to 
(one to many).

That should be the only diufference between the applications.

> I have just used -[no]brief option. but I didn't get what I want.

The identity is in the header above each sequence alignment in the 
default output.

There are other alignment output formats available with the -aformat option.

Can you give an example of what you would like to see. We probably 
already have a format in needle and needleall that gives what you need.


Peter Rice

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