Question+about+clustal+omega+and+orientation

2-10-13 I contacted the clustal omega team with this message. I am aligning some DNA, but I notice that Clustal Omega does not try to align the reverse complement of a sequence of the forward orientation does not align well. Is there a way to make Clustal Omega consider orientation? Also, if there is a way to the algorithm consider orientation, is there a way to indicate the orientaiton of the DNA fragments in the output? Lastly, if Clustal Omega cannot do these things, do you have some suggestions of a program that can? Thanks for any help and information you have to offer me!

reply https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/13cc88b7f4ecd03b Hi,

No, Clustal Omega doesn't do these things. Multiple sequence alignment tools of this class are more designed to align complete known coding sequences or gene products. For genomic alignments we have some pairwise tools for example promotorwise (under @http://www.ebi.ac.uk/Tools/psa/), but otherwise you are probably better off looking for dedicated assembly tools (for examples, see this list from our neighbours at WTSI: @http://www.sanger.ac.uk/resources/software/)

Regards,

Support@EMBL-EBI

My comments for myself It looks like Promoterwise can only align two sequences. I took a quick look at the Sanger Institute software and none of it looks too user friendly or I didn't try it since it only runs on Linux.