[This is offtopic, and I shouldn't be encouraging it] Michael James wrote: > I propose that the FASTA format be extended so that programs using it: > 1) Strip and store as a comment anything on a line after a # sign. > 2) Ignore lines with nothing [but whitespace] left after stripping. > > As far as blast is concerned > this would involve modifying formatdb > so it takes all such comments > and includes them in the existing ".nal" file. > No change needed to the main blastall binary > as this file already contains # comments. There is a lot more code out there than just blast which would require adjustment. We've all got a few favorite annotations we'd like to see in every header. Personally I need species info. Why not pick a less destructive route. Any code which writes a fasta file (called X) should feel free to put extra information into X.annot into the same directory. And any program that loads a fasta (named Y) should feel free to check for Y.annot in the same directory. May as well make it a valid XML file format while you're at it. I seem to recall parsing a lot of fairly regularly annotated fasta files that were annotated with /tag='value' in the comment line. This was also a nice solution, albeit some sort of a %39 escaping for the "'" character would have helped. And feel free to do whatever you like in-house. Its a dirty little secret that we've all kludged a few quick systems that simply would not die. > Your comments? you asked ;)