I have a number (~500) of 1-2kbp sequences which I'd like to align using clustalw; in this case the sequences are from transposable elements. The problem is that (obviously) the sequences have a distinct directionality, and the program I use to mine the sequences from a genomic contig set doesn't guarantee any particular orientation. My concern is that for some sequences I should be aligning the reverse complement, rather than the original orientation.
Is there a way in clustalw to get around this problem? Is there some other program that can put my sequences in the proper orientation before I align them with clustalw?
A quick example:
ATCGCGATATCG and CGATATCGCGAT can clearly be aligned, since the second sequence is the reverse complement of the first. If I ran clustalw with them as is, however, the alignment would be far from ideal.