showdb

 

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Function

Displays information on configured databases

Description

showdb displays a table with the names, contents and access methods of the sequence databases configured for your EMBOSS installation.

Usage

Here is a sample session with showdb

Display information on the currently available databases:


% showdb 
Displays information on configured databases

# Name           Type ID  Qry All Comment
# ============== ==== ==  === === =======
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   Genbank IDs
qanfasta         N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  EMBL flatfiles
qanflatall       N    OK  OK  OK  EMBL flatfiles
qanflatexc       N    OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  EMBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  GCG format EMBL
qangcgall        N    OK  OK  OK  GCG format EMBL
qangcgexc        N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  EMBL flatfiles
qanxflatall      N    OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  GCG format EMBL
qanxgcgall       N    OK  OK  OK  GCG format EMBL
qanxgcgexc       N    OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  PIR
qasrswww         N    OK  -   -   Remote SRS web server
qawfasta         N    OK  OK  OK  FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  PIR
tembl            N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  test sequence data
tgb              N    OK  -   -   Genbank IDs
tgenbank         N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

Example 2

Write the results to a file:


% showdb -outfile showdb.out 
Displays information on configured databases

Go to the output files for this example

Example 3

Display information on one explicit database:


% showdb -database tsw 
Displays information on configured databases

# Name         Type ID  Qry All Comment
# ============ ==== ==  === === =======
tsw            P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index

Go to the input files for this example

Example 4

Display information on the databases formatted in HTML:


% showdb -html 
Displays information on configured databases

NameTypeIDQryAllComment
twpPOK OK OK EMBL new in native format with EMBL CD-ROM index
qapblastPOK OK OK BLAST swissnew
qapblastallPOK OK OK BLAST swissnew, all fields indexed
qapblastsplitPOK OK OK BLAST swissnew split in 5 files
qapblastsplitexcPOK OK OK BLAST swissnew split in 5 files, not file 02
qapblastsplitincPOK OK OK BLAST swissnew split in 5 files, only file 02
qapfastaPOK OK OK FASTA file swissnew entries
qapflatPOK OK OK SpTrEmbl flatfile
qapflatallPOK OK OK SpTrEmbl flatfiles, all fields indexed
qapirPOK OK OK PIR
qapirallPOK OK OK PIR
qapirincPOK OK OK PIR
qapxfastaPOK OK OK FASTA file swissnew entries
qapxflatPOK OK OK Swissnew flatfiles
qaxpirPOK OK OK PIR
qaxpirallPOK OK OK PIR
qaxpirincPOK OK OK PIR
tpirPOK OK OK PIR using NBRF access for 4 files
tswPOK OK OK Swissprot native format with EMBL CD-ROM index
tswnewPOK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index
genbanksrsNOK - - Genbank IDs
qanfastaNOK OK OK FASTA file EMBL rodents
qanfastaallNOK OK OK FASTA file EMBL rodents, all fields indexed
qanflatNOK OK OK EMBL flatfiles
qanflatallNOK OK OK EMBL flatfiles
qanflatexcNOK OK OK EMBL flatfiles, no rodent file
qanflatincNOK OK OK EMBL flatfiles, only rodent file
qangcgNOK OK OK GCG format EMBL
qangcgallNOK OK OK GCG format EMBL
qangcgexcNOK OK OK GCG format EMBL without prokaryotes
qangcgincNOK OK OK GCG format EMBL only prokaryotes
qanxfastaNOK OK OK FASTA file EMBL rodents
qanxfastaallNOK OK OK FASTA file EMBL rodents, all fields indexed
qanxflatNOK OK OK EMBL flatfiles
qanxflatallNOK OK OK EMBL flatfiles, all fields indexed
qanxflatexcNOK OK OK EMBL flatfiles, no rodent file
qanxflatincNOK OK OK EMBL flatfiles, only rodent file
qanxgcgNOK OK OK GCG format EMBL
qanxgcgallNOK OK OK GCG format EMBL
qanxgcgexcNOK OK OK GCG format EMBL without prokaryotes
qanxgcgincNOK OK OK GCG format EMBL only prokaryotes
qapirexcNOK OK OK PIR
qasrswwwNOK - - Remote SRS web server
qawfastaNOK OK OK FASTA file wormpep entries
qawxfastaNOK OK OK FASTA file wormpep entries
qaxpirexcNOK OK OK PIR
temblNOK OK OK EMBL in native format with EMBL CD-ROM index
temblallN- - OK EMBL in native format with EMBL CD-ROM index
temblrestN- - OK EMBL in native format with EMBL CD-ROM index
temblvrtN- - OK EMBL in native format with EMBL CD-ROM index
testdbNOK OK OK test sequence data
tgbNOK - - Genbank IDs
tgenbankNOK OK OK GenBank in native format with EMBL CD-ROM index

Example 5

Display protein databases only:


% showdb -nonucleic 
Displays information on configured databases

# Name           Type ID  Qry All Comment
# ============== ==== ==  === === =======
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index

Example 6

Display the information with no headings:


% showdb -noheading 
Displays information on configured databases

twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   Genbank IDs
qanfasta         N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  EMBL flatfiles
qanflatall       N    OK  OK  OK  EMBL flatfiles
qanflatexc       N    OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  EMBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  GCG format EMBL
qangcgall        N    OK  OK  OK  GCG format EMBL
qangcgexc        N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  EMBL flatfiles
qanxflatall      N    OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  GCG format EMBL
qanxgcgall       N    OK  OK  OK  GCG format EMBL
qanxgcgexc       N    OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  PIR
qasrswww         N    OK  -   -   Remote SRS web server
qawfasta         N    OK  OK  OK  FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  PIR
tembl            N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  test sequence data
tgb              N    OK  -   -   Genbank IDs
tgenbank         N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

Example 7

Display just a list of the available database names:


% showdb -noheading -notype -noid -noquery -noall -nocomment -auto 

twp              
qapblast         
qapblastall      
qapblastsplit    
qapblastsplitexc 
qapblastsplitinc 
qapfasta         
qapflat          
qapflatall       
qapir            
qapirall         
qapirinc         
qapxfasta        
qapxflat         
qaxpir           
qaxpirall        
qaxpirinc        
tpir             
tsw              
tswnew           
genbanksrs       
qanfasta         
qanfastaall      
qanflat          
qanflatall       
qanflatexc       
qanflatinc       
qangcg           
qangcgall        
qangcgexc        
qangcginc        
qanxfasta        
qanxfastaall     
qanxflat         
qanxflatall      
qanxflatexc      
qanxflatinc      
qanxgcg          
qanxgcgall       
qanxgcgexc       
qanxgcginc       
qapirexc         
qasrswww         
qawfasta         
qawxfasta        
qaxpirexc        
tembl            
temblall         
temblrest        
temblvrt         
testdb           
tgb              
tgenbank         

Example 8

Display only the names and types:


% showdb -only -type 
Displays information on configured databases

twp              P    
qapblast         P    
qapblastall      P    
qapblastsplit    P    
qapblastsplitexc P    
qapblastsplitinc P    
qapfasta         P    
qapflat          P    
qapflatall       P    
qapir            P    
qapirall         P    
qapirinc         P    
qapxfasta        P    
qapxflat         P    
qaxpir           P    
qaxpirall        P    
qaxpirinc        P    
tpir             P    
tsw              P    
tswnew           P    
genbanksrs       N    
qanfasta         N    
qanfastaall      N    
qanflat          N    
qanflatall       N    
qanflatexc       N    
qanflatinc       N    
qangcg           N    
qangcgall        N    
qangcgexc        N    
qangcginc        N    
qanxfasta        N    
qanxfastaall     N    
qanxflat         N    
qanxflatall      N    
qanxflatexc      N    
qanxflatinc      N    
qanxgcg          N    
qanxgcgall       N    
qanxgcgexc       N    
qanxgcginc       N    
qapirexc         N    
qasrswww         N    
qawfasta         N    
qawxfasta        N    
qaxpirexc        N    
tembl            N    
temblall         N    
temblrest        N    
temblvrt         N    
testdb           N    
tgb              N    
tgenbank         N    

Example 9

Display everything


% showdb -full 
Displays information on configured databases

# Name           Type ID  Qry All Method    Fields            Defined Release Comment
# ============== ==== ==  === === ========= ================= ======= ======= =======
twp              P    OK  OK  OK  emblcd    des               global  16      EMBL new in native format with EMBL CD-ROM index
qapblast         P    OK  OK  OK  blast     -                 special         BLAST swissnew
qapblastall      P    OK  OK  OK  blast     sv,des            special         BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  blast     -                 special         BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  blast     -                 special         BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  blast     -                 special         BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  emblcd    -                 special         FASTA file swissnew entries
qapflat          P    OK  OK  OK  emblcd    -                 special         SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  emblcd    sv,des,org,key    special         SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  gcg       -                 special         PIR
qapirall         P    OK  OK  OK  gcg       des,org,key       special         PIR
qapirinc         P    OK  OK  OK  gcg       -                 special         PIR
qapxfasta        P    OK  OK  OK  emboss    -                 special         FASTA file swissnew entries
qapxflat         P    OK  OK  OK  emboss    -                 special         Swissnew flatfiles
qaxpir           P    OK  OK  OK  embossgcg -                 special         PIR
qaxpirall        P    OK  OK  OK  embossgcg des,org,key       special         PIR
qaxpirinc        P    OK  OK  OK  embossgcg -                 special         PIR
tpir             P    OK  OK  OK  gcg       des,org,key       special         PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  emblcd    sv,des,org,key    special 36      Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  emblcd    sv,des,org,key    special 37      SpTrEmbl as 3 files in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   srswww    gi,sv,des,org,key global          Genbank IDs
qanfasta         N    OK  OK  OK  emblcd    -                 special         FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  emblcd    sv,des            special         FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  emblcd    -                 special         EMBL flatfiles
qanflatall       N    OK  OK  OK  emblcd    -                 special         EMBL flatfiles
qanflatexc       N    OK  OK  OK  emblcd    -                 special         EMBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  emblcd    -                 special         EMBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  gcg       -                 special         GCG format EMBL
qangcgall        N    OK  OK  OK  gcg       sv,des,org,key    special         GCG format EMBL
qangcgexc        N    OK  OK  OK  gcg       -                 special         GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  gcg       -                 special         GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  emboss    -                 special         FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  emboss    sv,des            special         FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  emboss    -                 special         EMBL flatfiles
qanxflatall      N    OK  OK  OK  emboss    des,org,key       special         EMBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  emboss    -                 special         EMBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  emboss    -                 special         EMBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  embossgcg -                 special         GCG format EMBL
qanxgcgall       N    OK  OK  OK  embossgcg sv,des,org,key    special         GCG format EMBL
qanxgcgexc       N    OK  OK  OK  embossgcg -                 special         GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  embossgcg -                 special         GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  gcg       -                 special         PIR
qasrswww         N    OK  -   -   srswww    sv,des,org,key    special         Remote SRS web server
qawfasta         N    OK  OK  OK  emblcd    -                 special         FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  emboss    -                 special         FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  embossgcg -                 special         PIR
tembl            N    OK  OK  OK  emblcd    sv,des,org,key    special 57      EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  direct    sv,des,org,key    special 57      EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  direct    sv,des,org,key    special 57      EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  direct    sv,des,org,key    special 57      EMBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  emblcd    des               special 01      test sequence data
tgb              N    OK  -   -   srswww    sv,des,org,key    special         Genbank IDs
tgenbank         N    OK  OK  OK  emblcd    sv,des,org,key    special 01      GenBank in native format with EMBL CD-ROM index

Command line arguments

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers:
   -database           string     Name of a single database to give
                                  information on (Any string is accepted)
   -html               boolean    [N] Format output as an HTML table
   -[no]protein        boolean    [Y] Display protein databases
   -[no]nucleic        boolean    [Y] Display nucleic acid databases
   -full               boolean    [N] Display all columns
   -methods            boolean    [$(full)] This displays the access methods
                                  that can be used on this database, for all,
                                  query or ID access
   -fields             boolean    [$(full)] This displays the search fields
                                  that can be used on this database, other
                                  than the standard 'id' or 'acc' fields.
   -defined            boolean    [$(full)] This displays a short name for the
                                  file containing the database definition
   -release            boolean    [$(full)] Display 'release' column
   -outfile            outfile    [stdout] Output file name

   Advanced (Unprompted) qualifiers:
   -only               toggle     [N] This is a way of shortening the command
                                  line if you only want a few standard columns
                                  to be displayed. Instead of specifying:
                                  '-nohead -notype -noid -noquery -noall'
                                  to get only the comment output, you can
                                  specify
                                  '-only -comment'
   -heading            boolean    [@(!$(only))] Display column headings
   -type               boolean    [@(!$(only))] Display 'type' column
   -id                 boolean    [@(!$(only))] Display 'id' column
   -query              boolean    [@(!$(only))] Display 'qry' column
   -all                boolean    [@(!$(only))] Display 'all' column
   -comment            boolean    [@(!$(only))] Display 'comment' column

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers Allowed values Default
(none)
Additional (Optional) qualifiers Allowed values Default
-database Name of a single database to give information on Any string is accepted An empty string is accepted
-html Format output as an HTML table Boolean value Yes/No No
-[no]protein Display protein databases Boolean value Yes/No Yes
-[no]nucleic Display nucleic acid databases Boolean value Yes/No Yes
-full Display all columns Boolean value Yes/No No
-methods This displays the access methods that can be used on this database, for all, query or ID access Boolean value Yes/No $(full)
-fields This displays the search fields that can be used on this database, other than the standard 'id' or 'acc' fields. Boolean value Yes/No $(full)
-defined This displays a short name for the file containing the database definition Boolean value Yes/No $(full)
-release Display 'release' column Boolean value Yes/No $(full)
-outfile Output file name Output file stdout
Advanced (Unprompted) qualifiers Allowed values Default
-only This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment' Toggle value Yes/No No
-heading Display column headings Boolean value Yes/No @(!$(only))
-type Display 'type' column Boolean value Yes/No @(!$(only))
-id Display 'id' column Boolean value Yes/No @(!$(only))
-query Display 'qry' column Boolean value Yes/No @(!$(only))
-all Display 'all' column Boolean value Yes/No @(!$(only))
-comment Display 'comment' column Boolean value Yes/No @(!$(only))

Input file format

None.

Input files for usage example 3

'tsw' is a sequence entry in the example protein database 'tsw'

Output file format

Output files for usage example 2

File: showdb.out

# Name           Type ID  Qry All Comment
# ============== ==== ==  === === =======
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   Genbank IDs
qanfasta         N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  EMBL flatfiles
qanflatall       N    OK  OK  OK  EMBL flatfiles
qanflatexc       N    OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  EMBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  GCG format EMBL
qangcgall        N    OK  OK  OK  GCG format EMBL
qangcgexc        N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  EMBL flatfiles
qanxflatall      N    OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  GCG format EMBL
qanxgcgall       N    OK  OK  OK  GCG format EMBL
qanxgcgexc       N    OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  PIR
qasrswww         N    OK  -   -   Remote SRS web server
qawfasta         N    OK  OK  OK  FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  PIR
tembl            N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  test sequence data
tgb              N    OK  -   -   Genbank IDs
tgenbank         N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

The output is a simple table.

Type 'P' indicates that this is a Protein database.

Type 'N' indicates that this is a Nucleic database.

'OK' under ID, Qry or All indicates that that access method can be used on this database. A '-' indicates that you cannot access this database in that way.

Note that 'OK' does not mean that the database is working correctly. It simply means that showdb has read the database definition correctly and that this method of access to the database should be possible.

If you are setting up a new database, then you should check that it works correctly by extracting entries from it using seqret.

When the -html qualifier is specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are not output by this program as the table of databases is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user.

Data files

The databases are specified in the files "emboss.defaults" for site wide definitions, and "~/.embossrc" for the user's own settings.

Notes

EMBOSS provides excellent database support. All the common sequence formats you are likely to come across are supported. There are three basic levels of database query with different ways to search for and retrieve entries: entry A single entry specified by database ID or accession number is retrieved. For example "embl:x13776". query One or more entries matching a wildcard string in the USA are retrieved (this can be slow for some methods). For example you can specify all of the human PAX proteins in SWISS_PROT by: swissprot:pax*_human. all All entries are read sequentially from a database. For example to specify all entries in the database use embl:*.

One or more query levels may be available for a database depending on the database in question and how it has been setup and indexed. Each database and access method must be configured for it to be available for use. This involves editing one of the EMBOSS configuration files, either your own personal .embossrc or the installation-wide emboss.default file. The emboss.default file will typically contain the definitions of the test databases (tsw, tembl, tpir, etc) used in the usage examples for the application documentation and serve as example database definitions. For more information, see the EMBOSS Administrators Manual. You can run showdb to see the databases and access methods that have been configured successfully.

References

None.

Warnings

Where the string OK is given next to a database is listed in showdb output, this means showdb has read the database definition correctly and that this access method is in principle possible, in other words, the database has been configured correctly.. It does not mean that the database or access method are available or working correctly. You should check things are ok by running, for example, seqret to retrieve an entry.

Diagnostic Error Messages

"The database 'xyz' does not exist" You have supplied the name of a database with the -database qualifier, but that database does not exist as far as EMBOSS is concerned.

Exit status

It always exits with status 0, unless the above diagnostic message is displayed.

Known bugs

None noted.

See also

Program name Description
abiview Display the trace in an ABI sequencer file
cirdna Draws circular maps of DNA constructs
infoalign Display basic information about a multiple sequence alignment
infobase Return information on a given nucleotide base
inforesidue Return information on a given amino acid residue
infoseq Display basic information about sequences
lindna Draws linear maps of DNA constructs
pepnet Draw a helical net for a protein sequence
pepwheel Draw a helical wheel diagram for a protein sequence
prettyplot Draw a sequence alignment with pretty formatting
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
seealso Finds programs with similar function to a specified program
showalign Display a multiple sequence alignment in pretty format
showfeat Display features of a sequence in pretty format
showpep Displays protein sequences with features in pretty format
showseq Displays sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
textsearch Search the textual description of sequence(s)
tfm Displays full documentation for an application
whichdb Search all sequence databases for an entry and retrieve it
wossname Finds programs by keywords in their short description

Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Completed 6th August 1999.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None