What tools to perform alignment without adding gaps in?

Question

[biolab]

Hi everyone

I have about one hundred short sequences (each 20 nt long), and need to perform sequence alignment. I found both CLUSTALX and MUSCLE add gaps in the alignment. My aim is to cluster these sequences into different groups, and visualize the alignment. Could anyone help me to sort out this problem? Any of your suggestions will be much appreciated. THANKS in advance!

[brentp]

you mean multiple-sequence alignment, yes?

[pld]

Have you explored using something like Gblocks to remove alignment regions with gaps?

Answer 1

[Pierre Lindenbaum]

did you try to set a very high number for the cost of gap-open for those tools ?

for example in bwa mem :

-O INT     gap open penalty [6]

[biolab]

Hi Pierre, thanks a lot for your help, however, these short sequences are miRs from various species. Therefore, I do not have reference genome for mapping. Ideally I can visualize the alignment via some tools.

[Pierre Lindenbaum]

whatever the aligner is, clustalx have an option gap-open too: http://www.clustal.org/download/clustalx_help.html

Gap Open Penalty: the penalty for opening a gap in the alignment.

[MA]

To Pierre,

I am biolab, today my google account doesn't work, so I have to use Github account and answer section to reply to you. Thanks for your comments! I do find in CLUSTALX, the Profile Alignment Mode has gap penalty parameter.