I am creating a set of alignment output files from an XMFA (one per alignment), but I want to retain strandedness. Is there a format that will retain the strand? I could hack it so that it is on the FASTA defline but I want the strandedness to be preserved when running another BioPerl script.
For example, when I have a fasta defline with the strand
>sequence1 strand|+ AAAAAAAA >sequence2 strand|- AAAAAAAA
BioPerl will not retain the strand information. The output file will not tell me that sequence2 has been reverse-complimented. Is there a format that would retain this information?
edit Additionally, is there a format that would retain strandedness through this conversion and then through a refinement by ClustalW?