clark@MSHRI.UTORONTO.CA (02/10/90)
I am posting this message on behalf of somebody who aparently has only read-only access to the info-gcg newslist: /Hello Steve| /I deeply understand your complains about this non machine-readable /PROSITE. I recently put it in a machine readable Form for using it /with FIND from the GCG. /Of course there is this big problem with missing ambiguity support, /i tried to circumvent it by using multiple entries for degenerate /consensus sequences. This makes the file pretty long. Some pattern /were too degenerate (more then 1000 fold), i skipped these, but this /were only 4 or 5 of them. /If you are interested, i can mail the file to you or to any other /person. When i asked Amos Bairoch he told me that there were two more /official transcriptions of PROSITE into FIND-Format, but i don't know /the sources, so i use my own one. /I am not posting this letter to info-GCG because our mailer refuses to /send to BITNET addresses with a "-" sign in it. If you think that it is /appropriate you can forward this message to info-gcg. /Sincerely, / Kay Hofmann / Institut fuer Biochemie (med. Fakultaet) / Universitaet Koeln (FRG) / AKC01@DK0RRZK0 Does anyone know how to get around this problem of a mailer not liking the name of our newsgroup? Stephen Clark clark@mshri.utoronto.ca (Internet) sinai@utoroci (Netnorth/Bitnet) "We should be quite remiss not to emphasize that despite the popularity of secondary structural prediction schemes, and the almost ritual performance of these calculations, the information available from this is of limited reliability. This is true even of the best methods now known, and much more so of the less successful methods commonly available in sequence analysis packages. Running a secondary structure prediction on a newly-determined sequence just because everyone else does so, is to be deplored, and the fact that the results of such predictions are generally ignored is insufficient justification for doing and publishing them." - Arthur Lesk, 1988