TSPRINGER@BIONET-20.ARPA (05/31/88)
From: Timothy Springer <TSPRINGER@BIONET-20.ARPA> During a FASTP search of the SWISS-PROT library, ktup=1, the histogram of initial scores shows 3 scores 80 or better, while there is only one which appears in the following list of the best scoring sequences. This has happened before. What do you think is the matter? -------
SYEH@BIONET-20.ARPA (06/02/88)
From: BIONET <BIONET@BIONET-20.ARPA> Dear Tim, I have looked into this problem with XFASTP. It appears that XFASTP does not correctly swap high scoring sequences for low scoring sequences when the maximum number of kept scores (1000 for the DEC version) is reached. Thus the histogram would have the correct score record, if this is the case, and the list of scores would be missing some top scoring sequences. The version of FASTP which is accessed by FASTP-MAIL maintains a larger array of scores, and I have not encountered the same problem with it since I have not exceeded the maximum yet. In addition, the FASTP-MAIL version is more recent and may not have this program bug. To correct this problem, we are working to install a FASTA mail server. As you are aware, FASTA is a newer version of FASTP, and we are trying to focus our support on this version. Sorry for the inconvenience that this has caused you. This problem with XFASTP (and XFASTN) has only come to our attention within the last month. Sincerely, Spencer Yeh ARPAnet: bionet@bionet-20.arpa Scientific Consultant (for BIONET issues) or BIONET SYeh@bionet-20.arpa (415) 324-4363 -------