PERLMUTTER.HILLSON@BIONET-20.ARPA (04/02/88)
From: JAN HILLSON <PERLMUTTER.HILLSON@BIONET-20.ARPA> To whoever maintains the FASTP/N programs: When using a short sequence as a probe, the XFASTN program asks for a cutoff score, but appears to use its own suggested default no matter what you enter as a response. [For debugging: I used the single locus file "MODULE" to probe a few of the GENBANK sub-databases; MODULE is in my sub- directory.] -------
SYEH@BIONET-20.ARPA (04/05/88)
From: BIONET <BIONET@BIONET-20.ARPA> Dear Bionet User, Thank you for informing us of this potential bug in XFASTN. I will test this out, and if it is indeed a problem with the program, I will have it fixed. Sincerely, Spencer Yeh ARPAnet: SYeh@bionet-20.arpa or Scientific Consultant bionet@bionet-20.arpa BIONET (for BIONET problems) (415) 324-4363 -------
SYEH@BIONET-20.ARPA (04/05/88)
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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