Thanks David Bauer, for pulling me afloat. The dbxflat is now grinding and I am making a small set of Perl accessors.
I saw a broken link at http://emboss.sourceforge.net, so tried to see if there are more. The validator at W3C http://validator.w3.org/checklink gives a decent list in response to the EMBOSS link, with the "recursive" option on. Another little thing, but I might be wrong, is whether all applications are listed in groups? for example, I go here (from the home page), http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/groups.html and click about, hunting for seqret, but dont find (I wanted to see which other related programs there is to seqret). The "see also" tables give me that of course, but I didnt discover that at first. Finally question: I will build an accessor (in Perl) that invokes seqret for pulling out a genbank sub-sequence, often just a small piece, plus the features that overlap with this piece. Can EMBOSS do this, or must I pull the whole entry, parse and find the overlapping pieces in Perl? I am working on these sites, which are only guaranteed to work now and then, http://biobase.com:8000/UTHCT http://biobase.com:8000/RNAport http://biobase.com:8000/RRNA and I may use EMBOSS tools as part of a later query mechanism. For now I will be using EMBOSS for filling in the non-matches between the matches from a blast and other similarity reports, for zoom-able alignments and better overview. And so far it is going well with EMBOSS. Niels L _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
