dbiblast

[Qingjuan Gu]

>The answer is that you should use 'chromosome' as the wildcard 
>database name. Secondly, the author of dbiblast thinks there 
>might be some problems with the 2.4.1 version and this will 
>be corrected in 2.5.0 which is out soon. Thirdly, do not use 
>the very latest formatdb (NCBI have not yet released the 
>details of their index format so EMBOSS cannot index them). 

I did not use 'formatdb' for blast database, I just download from ncbi ftpsite "ftp://ftp.ncbi.nih.gov/blast/db/FormattedDatabases/" download and use gunzip and untar command to get these database. 

I follow you instruction, it failed also. Here is the interactive result: 
# ls -l 
total 434903 
-rwxr--r--   1 nobody   blast     76626843 Jul  4 22:09 patnt.nhr 
-rwxr--r--   1 nobody   blast      8066892 Jul  4 22:19 patnt.nin 
-rwxr--r--   1 nobody   blast      5377840 Jul  4 22:10 patnt.nnd 
-rwxr--r--   1 nobody   blast        21052 Jul  4 22:10 patnt.nni 
-rwxr--r--   1 nobody   blast    142820076 Jul  4 22:13 patnt.nsd 
-rwxr--r--   1 nobody   blast      2926655 Jul  4 22:19 patnt.nsi 
-rwxr--r--   1 nobody   blast     92506630 Jul  4 22:19 patnt.nsq 
-rwxr--r--   1 nobody   blast       119501 Jul  4 22:19 patnt.ntd 
-rwxr--r--   1 nobody   blast        17904 Jul  4 22:19 patnt.nti 
-rwxr--r--   1 nobody   blast    116819853 Jun 28 09:30 patnt.tar.gz 
# 
# dbiblast 
Index a BLAST database 
Database name: patnt 
Database directory [.]: 
Wildcard database filename [patnt]: patnt 
Release number [0.0]: 
Index date [00/00/00]: 
         N : nucleic 
         P : protein 
         ? : unknown 
Sequence type [unknown]: N 
         1 : wublast and setdb/pressdb 
         2 : formatdb 
         0 : unknown 
Blast index version [unknown]: 2 

   EMBOSS An error in dbiblast.c at line 333: 
No files selected 
# 
if i use patnt.nin in 'wildcard databse filename', that works without complain. but when I use seqret or other command to search the sequence, there are always error message: 

# ls -l 
total 435242 
-rwxr-xr-x   1 root     system         416 Jul 25 10:58 acnum.hit 
-rwxr-xr-x   1 root     system         742 Jul 25 10:58 acnum.trg 
-rwxr-xr-x   1 root     system         322 Jul 25 10:56 division.lkp 
-rwxr-xr-x   1 root     system      338334 Jul 25 10:58 entrynam.idx 
-rwxr--r--   1 nobody   blast     76626843 Jul  4 22:09 patnt.nhr 
-rwxr--r--   1 nobody   blast      8066892 Jul  4 22:19 patnt.nin 
-rwxr--r--   1 nobody   blast      5377840 Jul  4 22:10 patnt.nnd 
-rwxr--r--   1 nobody   blast        21052 Jul  4 22:10 patnt.nni 
-rwxr--r--   1 nobody   blast    142820076 Jul  4 22:13 patnt.nsd 
-rwxr--r--   1 nobody   blast      2926655 Jul  4 22:19 patnt.nsi 
-rwxr--r--   1 nobody   blast     92506630 Jul  4 22:19 patnt.nsq 
-rwxr--r--   1 nobody   blast       119501 Jul  4 22:19 patnt.ntd 
-rwxr--r--   1 nobody   blast        17904 Jul  4 22:19 patnt.nti 
-rwxr--r--   1 nobody   blast    116819853 Jun 28 09:30 patnt.tar.gz 
# seqret 
Reads and writes (returns) sequences 
Input sequence(s): patnt:E00007.1 
Error: BLAST Entry failed 
Error: Unable to read sequence 'patnt:E00007.1' 
Input sequence(s): patnt:E00007 
Error: BLAST Entry failed 
Error: Unable to read sequence 'patnt:E00007' 
# seqret 
Reads and writes (returns) sequences 
Input sequence(s): patnt:2168318 
Error: BLAST Entry failed 
Error: Unable to read sequence 'patnt:2168318' 
Input sequence(s): patnt:2168314 
Error: BLAST Entry failed 
Error: Unable to read sequence 'patnt:2168314' 
# 

In my emboss.default:
DB patnt [
        type: N
        method: blast
        format: ncbi
        dir: /db4/users/qgu/test/test_dbi
        file: patnt.*
        indexdir: /db4/users/qgu/test/test_dbi
        release: "1.0"
        comment: "patnt formatted database --BLAST NCBI"
]

Also, my fasta and genbank files works fine, only blast database can not work well. 

Your help will be highly appreciated. 

Grace