Question about clustal omega and orientation

2015-01-13

azim58 - 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&amp;shva=1#label/Career/13cc88b7f4ec
d03b
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.

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