Sorry for being really thick :o) BUT, how do you get the frequencies of the symbols at each position in the alignment?
I have: Distribution[] dist = DistributionTools.distOverAlignment(alignment, true); But can figure out how to access the frequencies I need. Cheers! :o) Nath > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > Sent: 19 May 2006 03:16 > To: [EMAIL PROTECTED] > Cc: [email protected] > Subject: Re: [Biojava-l] Alignment consensus calculation > > Hi - > > To get a Distribution[] over an alignment you could use > DistributionTools.distOverAlignment(a) or one of the other overloaded > methods. > > To get a consensus you could simply find the most frequent Symbol in each > Distribution. To make a more sophisticated consensus you could have > thresholds below which you would report an ambiguity. > > eg if: > > a = 0.50 > t = 0.40 > c = 0.0 > g = 1.0 > > Your routine would need to decide if the consensus should be 'a' or 'w' or > the IUPAC symbol for [atg] which I cannot remember. You would probably use > some sort of cutoff value. It might be a routine like this: > > public SymbolList consensus(Alignment a, double threshold){ > .... > } > > It might be a method that others find useful so please post it back to the > list. > > Hope this helps, > > - Mark > > Mark Schreiber > Research Investigator (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > > > > > "Nathan S. Haigh" <[EMAIL PROTECTED]> > Sent by: [EMAIL PROTECTED] > 05/18/2006 11:44 PM > Please respond to n.haigh > > > To: <[email protected]> > cc: (bcc: Mark Schreiber/GP/Novartis) > Subject: [Biojava-l] Alignment consensus calculation > > > I was wondering if there were any methods for generating a consensus > sequence for alignments? Or any suggestions for calculating the frequency > of > symbols at each position in an alignment. > > I had a look at the DistributionTools after seeing a past e-mail to the > list > but couldn't figure if this would do the job as I'm new to Java. > > Thanks > Nath > > -------------------------------------------------------------------------- > -- > ------ > Dr. Nathan S. Haigh > Bioinformatics PostDoctoral Research Associate > > Room B2 211 Tel: +44 (0)114 22 > 20112 > Department of Animal and Plant Sciences Mob: +44 (0)7742 > 533 > 569 > University of Sheffield Fax: +44 (0)114 22 > 20002 > Western Bank Web: > www.bioinf.shef.ac.uk > Sheffield > www.petraea.shef.ac.uk > S10 2TN > -------------------------------------------------------------------------- > -- > ------ > > > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 0620-2, 18/05/2006 > Tested on: 18/05/2006 16:44:01 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0620-2, 18/05/2006 Tested on: 19/05/2006 11:23:32 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
