pairwise alignments help, please - need to align several sequences to one (Aug/30/2005 )

Hi all,

I need to align each of several sequences to one other sequence; several pairwise alignments - just to clarify, I need to align 100 short sequences of to one long sequence, but I do not want the shorter sequences to be aligned to each other.

Could someone suggest a program to do this? I am somewhat familiar with clustal x, but can't seem to get it to do what I want it to.

Thanks!

Hi

Try multalin (http://prodes.toulouse.inra.fr/multalin/multalin.html), give a nice graphical presentation, but is pretty basic otherwise.

Bob

the alignment software calculate differences between sequences.... shorting the big sequences will not give any problem becouse the information always relies in the comparable positions.

Good luck

Giuseppe

LALIGN is very nice

http://www.infobiogen.fr/services/analyseq...n/lfastap_in.pl

Seb_

Hi people I have been trying to do a multiple sequence alignment and using the BCM Sequence/search lancher. Off-late I get message saying that it cannt take up the job as it has 20 jobs in queue. I have tried at various hours of the day and gives the same message. Does anybody know an alternate site for this. I also need the display to be in box format so it would be easy to look for (asking for too much) - I ave used this feature earliar at BCM now cannt find on my searches. Any clue

You could always use emboss and run with a simple perl script.
Look at Needle to implment the standard alignment, you can also then choose to go for global/local alignments by looking at the other alignment tools offered by emboss.

DPK


Emboss is the solution to most basic biology problems.