Hello, If I create two swiss-format protein sequence files by using seqret on an EMBOSS protein sequence DB, then use these two files as the input to water or needle, I have to use "-sprotein1 -sprotein2" - otherwise they are treated as DNA sequences.
In older versions of EMBOSS the files would automatically be treated as protein - I tried this out with a few legacy installations and the need to force the sequences to be protein appears to have been introduced in 4.1.0. I first noticed this problem when using 5.0.0, but version 4.0.0 automatically recognizes them as protein. Is this intentional? (i.e. to ensure that DNA sequences with lots of ambiguity codes don't get misinterpreted as protein). If not, then I'll post full details. best wishes, John Walshaw Department of Computational & Systems Biology John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
