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MSF as input to plotsimilarity

Mike Neubauer neubauer at bms.com
Thu Dec 1 19:38:01 EST 1994


In article 11466 at emba.uvm.edu, brianf at med.uvm.edu (Brian Foley) writes:
>	The documentation says that the output created by PILEUP 
>(the pileup.msf file) can be used as input to PLOTSIMILARITY.
>
>	However, this is not working for me.  PLOTSIM says it cannot
>read pileup.msf.  The documantation also says that all the sequences
>have to be the same length, and my PILEUP was of sequences of
>various lengths, gaps were introduced.  Could this be the problem?
>If so, how does one plot the similarity of proteins that have
>udergone deletions/insertions during evolution?
>
>
 
Brian,
   You must designate which sequences in the file pileup.msf are to be used by PLOTSIMILARITY.  You can select all of the sequences in the msf file by giving

pileup.msf{*}

the {*} (left-curly-q asterisk right-curly-q) designates all of the sequences in your file pileup.msf

good luck

Mike Neubauer




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