New FASTA versions available

Sam Rushing rushing at titan.ksc.nasa.gov
Tue Feb 22 15:35:11 EST 1994


In article <CL4F0I.6wG at murdoch.acc.Virginia.EDU>, wrp at dayhoff.med.Virginia.EDU (William R. Pearson) says:
>
>        A new release of the FASTA program package, version 1.7, is
>now available from virginia.EDU in pub/fasta as fasta17.shar(.Z).
>
>        This version replaces the "rdf2" and "rss" programs with
>"prdf" and "prss", which calculate more accurate estimates for the
>statistical significance of a similarity score based on the scores of
>randomly shuffled sequences.  The earlier "rdf2" and "rss" programs
>calculated a "z-value," which is not very informative if the
>distribution of similarity scores is not normal.  Sequence similarity
>scores for random sequences are distributed according to the extreme
>value distribution, which is quite different from the normal
>distribution, especially for high scores. Prss and prdf estimate the
>parameters of the extreme value distribution and use these parameters
>to calculate the probability that a score as good or better than the
>unshuffled sequence score will be obtained.  I appreciate the help of
>Stephen Altschul, who showed me the error of calculating "z-values",
>and the help of Phil Green, who provided the extreme value
>distribution estimation routine.
>
>        Statistical estimates based on the extreme value distribution
>are usually more conservative than earlier estimates based on
>"z-values."
>
>In addition, a bug in the alignment routines that caused error
>messages and core dumps on some machines has been fixed.  This bug has
>also been fixed in version 1.6. The new 1.6 version is available as
>fasta16c32.shar(.Z).
>
>Bill Pearson



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