From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Newsgroups: bionet.software
Subject: Re: GCG synchronisation problem
Date: 5 Jan 93 10:22:43 GMT
Distribution: bionet
Organization: EMBnet Switzerland [Basel]

PARSONS_A@snd01.pcr.co.uk writes:

>affects the quality of the results that I get?

This Problem is Lethal. 

>I was trying to search PIR using FASTA and got the following error :-

> *** ERROR in SQNext. Sequence reading is out of synchronization. 


>Any ideas what is going on?


You need to rerun dbindex and the problem should be fixed. 

Regards 
Reinhard 



> *** ERROR in SQNext. Sequence reading is out of synchronization. 

> 



>(Peptide) FASTA of: Ul08.Gcg  from: 1   to: 750  December 8, 1992  15:09
> TO: p:*  Sequences:        223  Symbols:     30,658  Word Size: 2


>Score Init1 Initn
><  2     0     0:
>   4     0     0:
>   6     0     0:
>   8     0     0:
>  10     0     0:
>  12     0     0:
>  14     0     0:
>  16     1     1:=
>  18     4     4:==
>  20    12    12:======
>  22    26    26:=============
>  24    21    21:===========
>  26    35    35:==================
>  28    30    30:===============
>  30    10    10:=====
>  32    44    43:======================
>  34     7     6:===-
>  36     4     2:=-
>  38    10     6:===--
>  40     7     3:==--
>  42     4     5:==+
>  44     2     2:=
>  46     1     1:=
>  48     5     6:===
>  50     0     2:+
>  52     0     1:+
>  54     0     1:+
>  56     0     1:+
>  58     0     0:
>  60     0     1:+
>  62     0     1:+
>  64     0     0:
>  66     0     1:+
>  68     0     1:+
>  70     0     0:
>  72     0     1:+
>  74     0     0:
>  76     0     0:
>  78     0     0:
>  80     0     0:
>> 80     0     0:
> mean initn score:  23.8 (2.83)
> mean init1 score:  23.8 (2.83)


>The best scores are:				            init1 initn opt

>Pir1:Cbms  Cytochrome b - Mouse mitochondrion (SGC1)          39    72    40
>Pir1:Cbrt  Cytochrome b - Rat mitochondrion (SGC1)            39    68    40
>Pir1:Cbqfr  Cytochrome b - Rhodospirillum rubrum              39    66    41
>Pir1:Cbhu  Cytochrome b - Human mitochondrion (SGC1)          37    62    39
>Pir1:Wmrz17  Cytochrome b6-f complex 17K protein - Rice c...  44    59    66
>Pir1:O4hud1  Debrisoquine 4-hydroxylase (EC 1.14.14.-) cy...  37    55    37
>Pir1:Cbbo  Cytochrome b - Bovine mitochondrion (SGC1)         39    54    40
>Pir1:Wmlv17  Cytochrome b6-f complex 17K protein - Liverw...  37    52    57
>Pir1:Cbxl  Cytochrome b - African clawed frog mitochondri...  38    49    42
>Pir1:Ccqfct  Cytochrome c' - Rhodocyclus tenuis               35    49    35
>Pir1:Cbboc6  Cytochrome b-c1 complex, 6.4K protein - Bovine   36    48    41
>Pir1:Cblv55  Cytochrome b559 component E - Liverwort (Mar...  47    47    50
>Pir1:Cbobe  Cytochrome b - Evening primrose mitochondrion     47    47    61
>Pir1:Cbnt55  Cytochrome b559 component E - Common tobacco...  47    47    50
>Pir1:Cbrz55  Cytochrome b559 component E - Rice chloroplast   47    47    50
>Pir1:Cbvf  Cytochrome b - Fava bean mitochondrion             47    47    61
>Pir1:Wmnt17  Cytochrome b6-f complex 17K protein - Common...  45    45    67
>Pir1:Ccrfpp  Cytochrome c' - Rhodobacter capsulatus           33    43    33
>Pir1:Cclm  Cytochrome c - Pacific lamprey                     43    43    46
>Pir1:Cbutb  Cytochrome b - Trypanosoma brucei mitochondri...  32    42    42
>Pir1:Rdbyun  Ubiquinol--cytochrome-c reductase (EC 1.10.2...  42    42    42
>Pir1:Wmsp17  Cytochrome b6-f complex 17K protein - Spinac...  41    41    67
>Pir1:Cbyb55  Cytochrome b559 component psbE - Synechocyst...  41    41    48
>Pir1:O4psz  Denitrification system component nirT - Pseud...  41    41    51
>Pir1:Ccps5a  Cytochrome c551 - Pseudomonas aeruginosa         40    40    41
>Pir1:Cbrz  Cytochrome b - Rice mitochondrion                  39    39    41
>Pir1:Cbzm  Cytochrome b - Maize mitochondrion                 39    39    41
>Pir1:Ccps5f  Cytochrome c551 - Pseudomonas fluorescens bi...  38    38    49
>Pir1:Cbbo5  Cytochrome b5 - Bovine                            38    38    52
>Pir1:Ccps5d  Cytochrome c551 - Pseudomonas sp.                38    38    49
>Pir1:Ccbf6  Cytochrome c6 - Yellow-green alga (Bumillerio...  37    37    39
>Pir1:Ccps5s  Cytochrome c551 - Pseudomonas stutzeri (stra...  37    37    52
>Pir1:Ccps5b  Cytochrome c551 precursor - Pseudomonas stut...  37    37    47
>Pir1:Wmkl17  Cytochrome b6-f complex 17K protein - Chlore...  36    36    38
>Pir1:Cctw5t  Cytochrome c552 - Thermus aquaticus              36    36    36
>Pir1:Cblv6  Cytochrome b6 - Liverwort (Marchantia polymor...  34    34    36
>Pir1:Ccck  Cytochrome c - Yeast (Issatchenkia orientalis)     33    33    36
>Pir1:Ccus  Cytochrome c - Smut fungus (Ustilago sphaerogena)  33    33    34
>Pir1:Cceg  Cytochrome c - Euglena gracilis                    33    33    41
>Pir1:Cchq  Cytochrome c - Yeast (Hansenula anomala)           33    33    37

>Aligning...
> CPU time:  0:00:19
> Output File: Ul08.Fasta
>  PARSONS_A    job terminated at  8-DEC-1992 15:13:16.77

>  Accounting information:
>  Buffered I/O count:             457         Peak working set size:   12603
>  Direct I/O count:              1919         Peak page file size:     21702
>  Page faults:                  15293         Mounted volumes:             0
>  Charged CPU time:           0 00:00:29.73   Elapsed time:     0 00:05:30.12
-- 
+----------------------------------+-------------------------------------+
|    Dr. Reinhard Doelz            | RFC     doelz@urz.unibas.ch         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142036::doelz      |
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