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<DIV><STRONG><FONT size=2>Hi, I am new in emboss db config. Need some help in
indexing blast db.</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>I have in dir following files:</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>-rw-rw-r-- 1
maoj Seqdb 190733
May 30 08:19 drosoph.nt.nhr<BR>-rw-rw-r-- 1
maoj Seqdb
14108 May 30 08:19 drosoph.nt.nin<BR>-rw-rw-r-- 1
maoj
Seqdb 9360 May 30 08:19
drosoph.nt.nnd<BR>-rw-rw-r-- 1 maoj
Seqdb 84 May 30
08:19 drosoph.nt.nni<BR>-rw-rw-r-- 1
maoj Seqdb 174584
May 30 08:19 drosoph.nt.nsd<BR>-rw-rw-r-- 1
maoj
Seqdb 3699 May 30 08:19
drosoph.nt.nsi<BR>-rw-rw-r-- 1 maoj
Seqdb 31368306 May 30 08:19
drosoph.nt.nsq</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>i believe these are files from NCBI and generated use
formatdb version 2.2.5. I run dbiblast in this directory:</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>Index a BLAST database<BR>Database name:
drosoph<BR>Database directory [.]: <BR>Wildcard database filename [drosoph]:
drosoph.nt.*<BR>Release number [0.0]: <BR>Index date [00/00/00]:
<BR> N :
nucleic<BR> P :
protein<BR> ? :
unknown<BR>Sequence type [unknown]:
N<BR> 1 : wublast and
setdb/pressdb<BR> 2 :
formatdb<BR> 0 :
unknown<BR>Blast index version [unknown]: 2</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>then I got many lines of the following
message:</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>Warning: Duplicate ID skipped:
'0€0€ €^DROSOPHILA' All hits will point to first ID
found</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>The following new files were
generated:</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>-rw-rw-r-- 1
maoj
Seqdb 322 May 30 10:44
division.lkp<BR>-rw-rw-r-- 1 maoj
Seqdb 496 May 30 10:44
entrynam.idx<BR>-rw-rw-r-- 1 maoj
Seqdb 300 May 30 10:44
acnum.trg<BR>-rw-rw-r-- 1 maoj
Seqdb 300 May 30 10:44
acnum.hit</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>I then edit my ~/.embossrc file by add the following
lines:</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>DB drosoph
[<BR> type:
N<BR> method:
blast<BR> format:
ncbi<BR> dir:
/data/maoj/emboss/db/blast/drosoph<BR>
indexdir:
/data/maoj/emboss/db/blast/drosoph<BR>
file: "drosoph.nt.*"<BR> release:
"0.0"<BR> comment: "blast
drosoph"<BR> ]</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>Then I run showdb:</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>% showdb</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>Displays information on the currently available
databases<BR># Name Type ID Qry
All Comment<BR># ==== ==== ==
=== === =======<BR>drosoph
N OK OK OK blast
drosoph</FONT></STRONG></DIV>
<DIV><STRONG><FONT
size=2>test
N OK OK OK Test DB</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>The test db is genbank format and was running
fine.</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>Then I run seqret:</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>% seqret</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>Reads and writes (returns) sequences<BR>Input
sequence(s): drosoph:A*<BR>Error: BLAST Query failed<BR>Error: Unable to read
sequence 'drosoph:A*'<BR>Input sequence(s): drosoph:*</FONT></STRONG></DIV>
<DIV> </DIV>
<DIV><STRONG><FONT size=2> EMBOSS An error in ajseqdb.c at line
4006:<BR>error reading file
/data/maoj/emboss/db/blast/drosoph/drosoph.nt.nhr</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>Please advise what I might did wrong.
</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>Thank you very much!!!</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV></BODY></HTML>