Path: utzoo!utgpu!water!watmath!uunet!ig!daemon
From: SYEH@BIONET-20.ARPA
Newsgroups: bionet.software.contrib
Subject: Re: A POSSIBLE BUG IN XFASTN
Message-ID: <5747@ig.ig.com>
Date: 4 Apr 88 19:20:44 GMT
Sender: daemon@presto.ig.com
Lines: 129

From: BIONET <BIONET@BIONET-20.ARPA>

Dear Bionet User,

I was not able to reproduce your problem with using cutoff values in
XFASTN.  I have included below a PHOTO session giving an example.
Make sure that you respond appropriately to the "How many scores would
you like to see ?" prompt.
 
Sincerely,

Spencer Yeh			ARPAnet: SYeh@bionet-20.arpa or
Scientific Consultant			 bionet@bionet-20.arpa
BIONET						(for BIONET problems)
(415) 324-4363

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[PHOTO:  Recording initiated  Mon 4-Apr-88 10:06AM]

@xfastn
 fastn [tops-20] searches a nucleotide sequence data bank
 test sequence file name: sample-10bp.seq
 library to be searched? (1 GenBank; 2 EMBL) [<cr>=1] 1
 
 GENBANK sequence files:

	 1.  Primate
	 2.  Rodent
	 3.  Other Mammalian
	 4.  Other Vertebrate
	 5.  Invertebrate
	 6.  Plant
	 7.  Eukaryotic Organelle
	 8.  Bacterial
	 9.  Structural RNA
	10.  Viral
	11.  Phage
	12.  Synthetic
	13.  Unannotated
 GENBANK sequence file number to search? (1 to 13) [<cr>=1] 11
 ktup? (1 to 6) [<cr>=4] 
 ktup set to 4

         1.  10BP      :  DEFINITION  Bacteriophage alpha-3 J gene.
         2.  20BP      :  DEFINITION  Bacteriophage alpha-3 J gene.
 sequence to analyze? (1 to 2) [<cr>=1]? 1

 10BP :   10 NT
 a 100 percent match with this query sequence has a score of 40
 enter a new cutoff value [<cr>=25]: 5
 sequence may be truncated
 sequence may be truncated
 sequence may be truncated
 sequence may be truncated

<  4    24 :============
   8     0 :
  12     0 :
  16    63 :================================
  20    43 :======================
  24    44 :======================
  28    27 :==============
  32     9 :=====
  36     4 :==
  40     1 :=
  44     0 :
  48     0 :
  52     0 :
  56     0 :
  60     0 :
  64     0 :
  68     0 :
  72     0 :
  76     0 :
  80     0 :
  84     0 :
  88     0 :
  92     0 :
  96     0 :
 100     0 :
 104     0 :
 108     0 :
 112     0 :
 116     0 :
 120     0 :
 124     0 :
 128     0 :
 132     0 :
 136     0 :
 140     0 :
 144     0 :
 148     0 :
 152     0 :
 156     0 :
 160     0 :
>160     0 :
 263498 residues in   215 sequences, mean score:  19.0 (8.24)
  191 scores better than 5 saved, ktup: 4, fact: 4 scan time:  0:00:32.39
 enter file name for results :  temp.results
 How many scores would you like to see? [<cr>=20]? 191
The best scores are:					    init,  opt
AL3J      : Bacteriophage alpha-3 J gene.                     40,   40
PX1       : Bacteriophage phi-X174, complete genome.          36,   36
S13CG     : Bacteriophage S13 circular DNA, complete genome.  36,   36
PMUB      : Bacteriophage Mu protein B gene, complete cds.    34,   34
PT4PSET   : Bacteriophage T4 pseT gene encoding polynucleoti  34,   34
LAMBDAZ   : Bacteriophage lambda cI gene                      32,   32
 sequence may be truncated
LAM       : Bacteriophage lambda, complete genome.            32,   32

...



PRD1ITR1  : Bacteriophage PRD1 5' inverted terminal repeat.   16,   22
PRD1ITR2  : Bacteriophage PRD1 3' inverted terminal repeat.   16,   16
KU1TR3    : bacteriophage ku1 3'-terminal region rna.         16,   16
PT3TRS1   : bacteriophage t3 5' end, terminally redundant se  16,   24
PT3PRMF   : Bacteriophage T3 class III promoter at 54.2% (or  16,   16
PT3PRMA   : bacteriophage t3 promoter region, at 16.1% of t3  16,   16
PT3PRMB   : bacteriophage t3 promoter region, at 1.2% of t3   16,   16
PR722ITR2 : Bacteriophage PR722 (from E.coli) 3' inverted te  16,   16
 Display alignments also [<cr>=Yes] no
Library scan:  0:00:32.39  total CPU time:  0:01:15.82
@pop

[PHOTO:  Recording terminated Mon 4-Apr-88 11:25AM]
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