Great, thanks ! > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > Sent: Wednesday, March 19, 2008 10:29 AM > To: Marc Logghe > Cc: [email protected] > Subject: Re: [EMBOSS] needle -nobrief > > > From a quick look at the code: > > > Longest identity: you're right i.e. > (Identical residues x 100)/(Length of Alignment - Total Number of Gaps > in Alignment) > > > > Shortest identity = number of identical residues * 100 / > length of longest original sequence > > > The similarity calculations are the same as the 'identical' ones > except that the number of identical residues is replaced by the > number of pairwise comparisons that have a positive score in > the comparison matrix. > > HTH > > Alan > > > > > > Hi all, > > > > I have checked the docs and googled around but I did not find an > > explanation for how the shortest_similarity or shortest_identity is > > calculated by needle (using the -nobrief option). > > > > For longest_identity it seems to be: > > > > (Identical residues x 100)/(Length of Alignment - Total Number of Gaps > > in Alignment) > > > > Thanks and regards, > > > > Marc > > > > > > > > > > _______________________________________________ > > EMBOSS mailing list > > [email protected] > > http://lists.open-bio.org/mailman/listinfo/emboss > > >
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