CSC

 
 
Tehdyt toimenpiteet
EMBOSS: showdb
showdb

 

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

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
# =============== ========== ==  === === =======
qapblast          Protein    OK  OK  OK  BLAST swissnew
qapblastall       Protein    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta          Protein    OK  OK  OK  FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  PIR
qapirall          Protein    OK  OK  OK  PIR
qapirinc          Protein    OK  OK  OK  PIR
qapxfasta         Protein    OK  OK  OK  FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  PIR
qaxpirall         Protein    OK  OK  OK  PIR
qaxpirinc         Protein    OK  OK  OK  PIR
tpir              Protein    OK  OK  OK  PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew            Protein    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
qanfasta          Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanfastaall       Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat           Nucleotide OK  OK  OK  EMBL flatfiles
qanflatall        Nucleotide OK  OK  OK  EMBL flatfiles
qanflatexc        Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc        Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qangcg            Nucleotide OK  OK  OK  GCG format EMBL
qangcgall         Nucleotide OK  OK  OK  GCG format EMBL
qangcgexc         Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc         Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta         Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanxfastaall      Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat          Nucleotide OK  OK  OK  EMBL flatfiles
qanxflatall       Nucleotide OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc       Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg           Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgall        Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgexc        Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc        Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc          Nucleotide OK  OK  OK  PIR
qasrswww          Nucleotide OK  OK  OK  Remote SRS web server
qawfasta          Nucleotide OK  OK  OK  FASTA file wormpep entries
qawxfasta         Nucleotide OK  OK  OK  FASTA file wormpep entries
qaxpirexc         Nucleotide OK  OK  OK  PIR
tembl             Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblrest         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblvrt          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
tensembldasgrch37 Nucleotide OK  -   -   Homo_sapiens Reference server based on GRCh37 assembly
testdb            Nucleotide OK  OK  OK  test sequence data
tgb               Nucleotide OK  OK  OK  Genbank IDs
tgenbank          Nucleotide OK  OK  OK  GenBank in native format with EMBL CD-ROM index
tgenedashuman     Nucleotide OK  -   -   The Ensembl human Gene_ID reference source
tflybase          Features   OK  -   -   
tgenedb           Features   OK  -   -   
ttax              Taxonomy   OK  OK  OK  
taxon             Taxonomy   OK  OK  OK  
drcat             Resource   OK  OK  OK  
tedam             Obo        OK  OK  OK  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  EDAM using dbxobo test indexes
eco               Obo        OK  OK  OK  
edam              Obo        OK  OK  OK  
go                Obo        OK  OK  OK  
pw                Obo        OK  OK  OK  
ro                Obo        OK  OK  OK  
so                Obo        OK  OK  OK  

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            Protein 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
qapblastProteinOK OK OK BLAST swissnew
qapblastallProteinOK OK OK BLAST swissnew, all fields indexed
qapblastsplitProteinOK OK OK BLAST swissnew split in 5 files
qapblastsplitexcProteinOK OK OK BLAST swissnew split in 5 files, not file 02
qapblastsplitincProteinOK OK OK BLAST swissnew split in 5 files, only file 02
qapfastaProteinOK OK OK FASTA file swissnew entries
qapflatProteinOK OK OK SpTrEmbl flatfile
qapflatallProteinOK OK OK SpTrEmbl flatfiles, all fields indexed
qapirProteinOK OK OK PIR
qapirallProteinOK OK OK PIR
qapirincProteinOK OK OK PIR
qapxfastaProteinOK OK OK FASTA file swissnew entries
qapxflatProteinOK OK OK Swissnew flatfiles
qaxpirProteinOK OK OK PIR
qaxpirallProteinOK OK OK PIR
qaxpirincProteinOK OK OK PIR
tpirProteinOK OK OK PIR using NBRF access for 4 files
tswProteinOK OK OK Swissprot native format with EMBL CD-ROM index
tswnewProteinOK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index
qanfastaNucleotideOK OK OK FASTA file EMBL rodents
qanfastaallNucleotideOK OK OK FASTA file EMBL rodents, all fields indexed
qanflatNucleotideOK OK OK EMBL flatfiles
qanflatallNucleotideOK OK OK EMBL flatfiles
qanflatexcNucleotideOK OK OK EMBL flatfiles, no rodent file
qanflatincNucleotideOK OK OK EMBL flatfiles, only rodent file
qangcgNucleotideOK OK OK GCG format EMBL
qangcgallNucleotideOK OK OK GCG format EMBL
qangcgexcNucleotideOK OK OK GCG format EMBL without prokaryotes
qangcgincNucleotideOK OK OK GCG format EMBL only prokaryotes
qanxfastaNucleotideOK OK OK FASTA file EMBL rodents
qanxfastaallNucleotideOK OK OK FASTA file EMBL rodents, all fields indexed
qanxflatNucleotideOK OK OK EMBL flatfiles
qanxflatallNucleotideOK OK OK EMBL flatfiles, all fields indexed
qanxflatexcNucleotideOK OK OK EMBL flatfiles, no rodent file
qanxflatincNucleotideOK OK OK EMBL flatfiles, only rodent file
qanxgcgNucleotideOK OK OK GCG format EMBL
qanxgcgallNucleotideOK OK OK GCG format EMBL
qanxgcgexcNucleotideOK OK OK GCG format EMBL without prokaryotes
qanxgcgincNucleotideOK OK OK GCG format EMBL only prokaryotes
qapirexcNucleotideOK OK OK PIR
qasrswwwNucleotideOK OK OK Remote SRS web server
qawfastaNucleotideOK OK OK FASTA file wormpep entries
qawxfastaNucleotideOK OK OK FASTA file wormpep entries
qaxpirexcNucleotideOK OK OK PIR
temblNucleotideOK OK OK EMBL in native format with EMBL CD-ROM index
temblallNucleotideOK OK OK EMBL in native format with EMBL CD-ROM index
temblrestNucleotideOK OK OK EMBL in native format with EMBL CD-ROM index
temblvrtNucleotideOK OK OK EMBL in native format with EMBL CD-ROM index
tensembldasgrch37NucleotideOK - - Homo_sapiens Reference server based on GRCh37 assembly
testdbNucleotideOK OK OK test sequence data
tgbNucleotideOK OK OK Genbank IDs
tgenbankNucleotideOK OK OK GenBank in native format with EMBL CD-ROM index
tgenedashumanNucleotideOK - - The Ensembl human Gene_ID reference source
tflybaseFeaturesOK - -
tgenedbFeaturesOK - -
ttaxTaxonomyOK OK OK
taxonTaxonomyOK OK OK
drcatResourceOK OK OK
tedamOboOK OK OK EDAM using dbxedam test indexes
toboOboOK OK OK EDAM using dbxobo test indexes
ecoOboOK OK OK
edamOboOK OK OK
goOboOK OK OK
pwOboOK OK OK
roOboOK OK OK
soOboOK OK OK

Example 5

Display protein databases only:


% showdb -nonucleic 
Displays information on configured databases

# Name            Type       ID  Qry All Comment
# =============== ========== ==  === === =======
qapblast          Protein    OK  OK  OK  BLAST swissnew
qapblastall       Protein    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta          Protein    OK  OK  OK  FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  PIR
qapirall          Protein    OK  OK  OK  PIR
qapirinc          Protein    OK  OK  OK  PIR
qapxfasta         Protein    OK  OK  OK  FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  PIR
qaxpirall         Protein    OK  OK  OK  PIR
qaxpirinc         Protein    OK  OK  OK  PIR
tpir              Protein    OK  OK  OK  PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew            Protein    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
tflybase          Features   OK  -   -   
tgenedb           Features   OK  -   -   
ttax              Taxonomy   OK  OK  OK  
taxon             Taxonomy   OK  OK  OK  
drcat             Resource   OK  OK  OK  
tedam             Obo        OK  OK  OK  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  EDAM using dbxobo test indexes
eco               Obo        OK  OK  OK  
edam              Obo        OK  OK  OK  
go                Obo        OK  OK  OK  
pw                Obo        OK  OK  OK  
ro                Obo        OK  OK  OK  
so                Obo        OK  OK  OK  

Example 6

Display the information with no headings:


% showdb -noheading 
Displays information on configured databases

qapblast          Protein    OK  OK  OK  BLAST swissnew
qapblastall       Protein    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta          Protein    OK  OK  OK  FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  PIR
qapirall          Protein    OK  OK  OK  PIR
qapirinc          Protein    OK  OK  OK  PIR
qapxfasta         Protein    OK  OK  OK  FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  PIR
qaxpirall         Protein    OK  OK  OK  PIR
qaxpirinc         Protein    OK  OK  OK  PIR
tpir              Protein    OK  OK  OK  PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew            Protein    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
qanfasta          Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanfastaall       Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat           Nucleotide OK  OK  OK  EMBL flatfiles
qanflatall        Nucleotide OK  OK  OK  EMBL flatfiles
qanflatexc        Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc        Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qangcg            Nucleotide OK  OK  OK  GCG format EMBL
qangcgall         Nucleotide OK  OK  OK  GCG format EMBL
qangcgexc         Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc         Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta         Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanxfastaall      Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat          Nucleotide OK  OK  OK  EMBL flatfiles
qanxflatall       Nucleotide OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc       Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg           Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgall        Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgexc        Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc        Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc          Nucleotide OK  OK  OK  PIR
qasrswww          Nucleotide OK  OK  OK  Remote SRS web server
qawfasta          Nucleotide OK  OK  OK  FASTA file wormpep entries
qawxfasta         Nucleotide OK  OK  OK  FASTA file wormpep entries
qaxpirexc         Nucleotide OK  OK  OK  PIR
tembl             Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblrest         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblvrt          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
tensembldasgrch37 Nucleotide OK  -   -   Homo_sapiens Reference server based on GRCh37 assembly
testdb            Nucleotide OK  OK  OK  test sequence data
tgb               Nucleotide OK  OK  OK  Genbank IDs
tgenbank          Nucleotide OK  OK  OK  GenBank in native format with EMBL CD-ROM index
tgenedashuman     Nucleotide OK  -   -   The Ensembl human Gene_ID reference source
tflybase          Features   OK  -   -   
tgenedb           Features   OK  -   -   
ttax              Taxonomy   OK  OK  OK  
taxon             Taxonomy   OK  OK  OK  
drcat             Resource   OK  OK  OK  
tedam             Obo        OK  OK  OK  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  EDAM using dbxobo test indexes
eco               Obo        OK  OK  OK  
edam              Obo        OK  OK  OK  
go                Obo        OK  OK  OK  
pw                Obo        OK  OK  OK  
ro                Obo        OK  OK  OK  
so                Obo        OK  OK  OK  

Example 7

Display just a list of the available database names:


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

qapblast          
qapblastall       
qapblastsplit     
qapblastsplitexc  
qapblastsplitinc  
qapfasta          
qapflat           
qapflatall        
qapir             
qapirall          
qapirinc          
qapxfasta         
qapxflat          
qaxpir            
qaxpirall         
qaxpirinc         
tpir              
tsw               
tswnew            
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          
tensembldasgrch37 
testdb            
tgb               
tgenbank          
tgenedashuman     
tflybase          
tgenedb           
ttax              
taxon             
drcat             
tedam             
tobo              
eco               
edam              
go                
pw                
ro                
so                

Example 8

Display only the names and types:


% showdb -only -type 
Displays information on configured databases

qapblast          Protein    
qapblastall       Protein    
qapblastsplit     Protein    
qapblastsplitexc  Protein    
qapblastsplitinc  Protein    
qapfasta          Protein    
qapflat           Protein    
qapflatall        Protein    
qapir             Protein    
qapirall          Protein    
qapirinc          Protein    
qapxfasta         Protein    
qapxflat          Protein    
qaxpir            Protein    
qaxpirall         Protein    
qaxpirinc         Protein    
tpir              Protein    
tsw               Protein    
tswnew            Protein    
qanfasta          Nucleotide 
qanfastaall       Nucleotide 
qanflat           Nucleotide 
qanflatall        Nucleotide 
qanflatexc        Nucleotide 
qanflatinc        Nucleotide 
qangcg            Nucleotide 
qangcgall         Nucleotide 
qangcgexc         Nucleotide 
qangcginc         Nucleotide 
qanxfasta         Nucleotide 
qanxfastaall      Nucleotide 
qanxflat          Nucleotide 
qanxflatall       Nucleotide 
qanxflatexc       Nucleotide 
qanxflatinc       Nucleotide 
qanxgcg           Nucleotide 
qanxgcgall        Nucleotide 
qanxgcgexc        Nucleotide 
qanxgcginc        Nucleotide 
qapirexc          Nucleotide 
qasrswww          Nucleotide 
qawfasta          Nucleotide 
qawxfasta         Nucleotide 
qaxpirexc         Nucleotide 
tembl             Nucleotide 
temblall          Nucleotide 
temblrest         Nucleotide 
temblvrt          Nucleotide 
tensembldasgrch37 Nucleotide 
testdb            Nucleotide 
tgb               Nucleotide 
tgenbank          Nucleotide 
tgenedashuman     Nucleotide 
tflybase          Features   
tgenedb           Features   
ttax              Taxonomy   
taxon             Taxonomy   
drcat             Resource   
tedam             Obo        
tobo              Obo        
eco               Obo        
edam              Obo        
go                Obo        
pw                Obo        
ro                Obo        
so                Obo        

Example 9

Display everything


% showdb -full 
Displays information on configured databases

# Name            Type       ID  Qry All Method    Fields                                                                                         Defined  Release Comment
# =============== ========== ==  === === ========= ============================================================================================== ======== ======= =======
qapblast          Protein    OK  OK  OK  blast     -                                                                                              special          BLAST swissnew
qapblastall       Protein    OK  OK  OK  blast     sv,des                                                                                         special          BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  blast     -                                                                                              special          BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  blast     -                                                                                              special          BLAST swissnew split in 5 files, not file 02
qapblastsplitinc  Protein    OK  OK  OK  blast     -                                                                                              special          BLAST swissnew split in 5 files, only file 02
qapfasta          Protein    OK  OK  OK  emblcd    -                                                                                              special          FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  emblcd    -                                                                                              special          SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  emblcd    sv,des,org,key                                                                                 special          SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  gcg       -                                                                                              special          PIR
qapirall          Protein    OK  OK  OK  gcg       des,org,key                                                                                    special          PIR
qapirinc          Protein    OK  OK  OK  gcg       -                                                                                              special          PIR
qapxfasta         Protein    OK  OK  OK  emboss    -                                                                                              special          FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  emboss    -                                                                                              special          Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  embossgcg -                                                                                              special          PIR
qaxpirall         Protein    OK  OK  OK  embossgcg des,org,key                                                                                    special          PIR
qaxpirinc         Protein    OK  OK  OK  embossgcg -                                                                                              special          PIR
tpir              Protein    OK  OK  OK  gcg       des,org,key                                                                                    special          PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  emblcd    id,acc,sv,des,org,key                                                                          special  36      Swissprot native format with EMBL CD-ROM index
tswnew            Protein    OK  OK  OK  emblcd    sv,des,org,key                                                                                 special  37      SpTrEmbl as 3 files in native format with EMBL CD-ROM index
qanfasta          Nucleotide OK  OK  OK  emblcd    -                                                                                              special          FASTA file EMBL rodents
qanfastaall       Nucleotide OK  OK  OK  emblcd    sv,des                                                                                         special          FASTA file EMBL rodents, all fields indexed
qanflat           Nucleotide OK  OK  OK  emblcd    -                                                                                              special          EMBL flatfiles
qanflatall        Nucleotide OK  OK  OK  emblcd    -                                                                                              special          EMBL flatfiles
qanflatexc        Nucleotide OK  OK  OK  emblcd    -                                                                                              special          EMBL flatfiles, no rodent file
qanflatinc        Nucleotide OK  OK  OK  emblcd    -                                                                                              special          EMBL flatfiles, only rodent file
qangcg            Nucleotide OK  OK  OK  gcg       -                                                                                              special          GCG format EMBL
qangcgall         Nucleotide OK  OK  OK  gcg       sv,des,org,key                                                                                 special          GCG format EMBL
qangcgexc         Nucleotide OK  OK  OK  gcg       -                                                                                              special          GCG format EMBL without prokaryotes
qangcginc         Nucleotide OK  OK  OK  gcg       -                                                                                              special          GCG format EMBL only prokaryotes
qanxfasta         Nucleotide OK  OK  OK  emboss    -                                                                                              special          FASTA file EMBL rodents
qanxfastaall      Nucleotide OK  OK  OK  emboss    sv,des                                                                                         special          FASTA file EMBL rodents, all fields indexed
qanxflat          Nucleotide OK  OK  OK  emboss    -                                                                                              special          EMBL flatfiles
qanxflatall       Nucleotide OK  OK  OK  emboss    des,org,key                                                                                    special          EMBL flatfiles, all fields indexed
qanxflatexc       Nucleotide OK  OK  OK  emboss    -                                                                                              special          EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide OK  OK  OK  emboss    -                                                                                              special          EMBL flatfiles, only rodent file
qanxgcg           Nucleotide OK  OK  OK  embossgcg -                                                                                              special          GCG format EMBL
qanxgcgall        Nucleotide OK  OK  OK  embossgcg sv,des,org,key                                                                                 special          GCG format EMBL
qanxgcgexc        Nucleotide OK  OK  OK  embossgcg -                                                                                              special          GCG format EMBL without prokaryotes
qanxgcginc        Nucleotide OK  OK  OK  embossgcg -                                                                                              special          GCG format EMBL only prokaryotes
qapirexc          Nucleotide OK  OK  OK  gcg       -                                                                                              special          PIR
qasrswww          Nucleotide OK  OK  OK  srswww    sv,des,org,key                                                                                 special          Remote SRS web server
qawfasta          Nucleotide OK  OK  OK  emblcd    -                                                                                              special          FASTA file wormpep entries
qawxfasta         Nucleotide OK  OK  OK  emboss    -                                                                                              special          FASTA file wormpep entries
qaxpirexc         Nucleotide OK  OK  OK  embossgcg -                                                                                              special          PIR
tembl             Nucleotide OK  OK  OK  emblcd    sv,des,org,key                                                                                 special  57      EMBL in native format with EMBL CD-ROM index
temblall          Nucleotide OK  OK  OK  direct    sv,des,org,key                                                                                 special  57      EMBL in native format with EMBL CD-ROM index
temblrest         Nucleotide OK  OK  OK  direct    sv,des,org,key                                                                                 special  57      EMBL in native format with EMBL CD-ROM index
temblvrt          Nucleotide OK  OK  OK  direct    sv,des,org,key                                                                                 special  57      EMBL in native format with EMBL CD-ROM index
tensembldasgrch37 Nucleotide OK  -   -   das       -                                                                                              special          Homo_sapiens Reference server based on GRCh37 assembly
testdb            Nucleotide OK  OK  OK  emblcd    des                                                                                            special  01      test sequence data
tgb               Nucleotide OK  OK  OK  srswww    sv,des,org,key                                                                                 special          Genbank IDs
tgenbank          Nucleotide OK  OK  OK  emblcd    sv,des,org,key                                                                                 special  01      GenBank in native format with EMBL CD-ROM index
tgenedashuman     Nucleotide OK  -   -   das       -                                                                                              special          The Ensembl human Gene_ID reference source
tflybase          Features   OK  -   -   chado(id) uniquename                                                                                     special          
tgenedb           Features   OK  -   -   chado(id) uniquename                                                                                     special          
ttax              Taxonomy   OK  OK  OK  embosstax id,acc,nam,rnk,up,gc,mgc                                                                       special          
taxon             Taxonomy   OK  OK  OK  embosstax id,acc,tax,rnk,up,gc,mgc                                                                       standard         
drcat             Resource   OK  OK  OK  emboss    id,acc,nam,des,url,cat,edat,efmt,eid,etpc,xref,qout,qfmt,qin,qurl,cc,rest,soap,stat,xref,taxid standard         
tedam             Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                    special  beta11  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                    special  beta11  EDAM using dbxobo test indexes
eco               Obo        OK  OK  OK  emboss    id,acc,nam,isa,des                                                                             standard         
edam              Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc                                    standard         
go                Obo        OK  OK  OK  emboss    id,acc,nam,isa,des,ns                                                                          standard         
pw                Obo        OK  OK  OK  emboss    id,acc,nam,isa,des                                                                             standard         
ro                Obo        OK  OK  OK  emboss    id,acc,nam,isa,des                                                                             standard         
so                Obo        OK  OK  OK  emboss    id,acc,nam,isa,des                                                                             standard         

Command line arguments

Displays information on configured databases
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers:
   -database           string     Name of a single database to give
                                  information on (Any string)
   -html               boolean    [N] Format output as an HTML table
   -[no]protein        boolean    [Y] Display protein databases
   -[no]nucleic        boolean    [Y] Display nucleotide databases
   -[no]sequence       boolean    [Y] Display general sequence databases
   -[no]feature        boolean    [Y] Display feature annotation databases
   -[no]text           boolean    [Y] Display text databases
   -[no]taxonomy       boolean    [Y] Display taxonomy databases
   -[no]resource       boolean    [Y] Display resource databases
   -[no]assembly       boolean    [Y] Display sequence assembly databases
   -[no]obo            boolean    [Y] Display obo bio-ontology 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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
(none)
Additional (Optional) qualifiers
-database string Name of a single database to give information on Any string  
-html boolean Format output as an HTML table Boolean value Yes/No No
-[no]protein boolean Display protein databases Boolean value Yes/No Yes
-[no]nucleic boolean Display nucleotide databases Boolean value Yes/No Yes
-[no]sequence boolean Display general sequence databases Boolean value Yes/No Yes
-[no]feature boolean Display feature annotation databases Boolean value Yes/No Yes
-[no]text boolean Display text databases Boolean value Yes/No Yes
-[no]taxonomy boolean Display taxonomy databases Boolean value Yes/No Yes
-[no]resource boolean Display resource databases Boolean value Yes/No Yes
-[no]assembly boolean Display sequence assembly databases Boolean value Yes/No Yes
-[no]obo boolean Display obo bio-ontology databases Boolean value Yes/No Yes
-full boolean Display all columns Boolean value Yes/No No
-methods boolean This displays the access methods that can be used on this database, for all, query or ID access Boolean value Yes/No $(full)
-fields boolean 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 boolean This displays a short name for the file containing the database definition Boolean value Yes/No $(full)
-release boolean Display 'release' column Boolean value Yes/No $(full)
-outfile outfile Output file name Output file stdout
Advanced (Unprompted) qualifiers
-only toggle This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment' Toggle value Yes/No No
-heading boolean Display column headings Boolean value Yes/No @(!$(only))
-type boolean Display 'type' column Boolean value Yes/No @(!$(only))
-id boolean Display 'id' column Boolean value Yes/No @(!$(only))
-query boolean Display 'qry' column Boolean value Yes/No @(!$(only))
-all boolean Display 'all' column Boolean value Yes/No @(!$(only))
-comment boolean Display 'comment' column Boolean value Yes/No @(!$(only))
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

showdb examines the databases defined for this EMBOSS installation and for the current user.

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
# =============== ========== ==  === === =======
qapblast          Protein    OK  OK  OK  BLAST swissnew
qapblastall       Protein    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit     Protein    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc  Protein    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta          Protein    OK  OK  OK  FASTA file swissnew entries
qapflat           Protein    OK  OK  OK  SpTrEmbl flatfile
qapflatall        Protein    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir             Protein    OK  OK  OK  PIR
qapirall          Protein    OK  OK  OK  PIR
qapirinc          Protein    OK  OK  OK  PIR
qapxfasta         Protein    OK  OK  OK  FASTA file swissnew entries
qapxflat          Protein    OK  OK  OK  Swissnew flatfiles
qaxpir            Protein    OK  OK  OK  PIR
qaxpirall         Protein    OK  OK  OK  PIR
qaxpirinc         Protein    OK  OK  OK  PIR
tpir              Protein    OK  OK  OK  PIR using NBRF access for 4 files
tsw               Protein    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew            Protein    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
qanfasta          Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanfastaall       Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat           Nucleotide OK  OK  OK  EMBL flatfiles
qanflatall        Nucleotide OK  OK  OK  EMBL flatfiles
qanflatexc        Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc        Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qangcg            Nucleotide OK  OK  OK  GCG format EMBL
qangcgall         Nucleotide OK  OK  OK  GCG format EMBL
qangcgexc         Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc         Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta         Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanxfastaall      Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat          Nucleotide OK  OK  OK  EMBL flatfiles
qanxflatall       Nucleotide OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc       Nucleotide OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg           Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgall        Nucleotide OK  OK  OK  GCG format EMBL
qanxgcgexc        Nucleotide OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc        Nucleotide OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc          Nucleotide OK  OK  OK  PIR
qasrswww          Nucleotide OK  OK  OK  Remote SRS web server
qawfasta          Nucleotide OK  OK  OK  FASTA file wormpep entries
qawxfasta         Nucleotide OK  OK  OK  FASTA file wormpep entries
qaxpirexc         Nucleotide OK  OK  OK  PIR
tembl             Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblrest         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblvrt          Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM index
tensembldasgrch37 Nucleotide OK  -   -   Homo_sapiens Reference server based on GRCh37 assembly
testdb            Nucleotide OK  OK  OK  test sequence data
tgb               Nucleotide OK  OK  OK  Genbank IDs
tgenbank          Nucleotide OK  OK  OK  GenBank in native format with EMBL CD-ROM index
tgenedashuman     Nucleotide OK  -   -   The Ensembl human Gene_ID reference source
tflybase          Features   OK  -   -   
tgenedb           Features   OK  -   -   
ttax              Taxonomy   OK  OK  OK  
taxon             Taxonomy   OK  OK  OK  
drcat             Resource   OK  OK  OK  
tedam             Obo        OK  OK  OK  EDAM using dbxedam test indexes
tobo              Obo        OK  OK  OK  EDAM using dbxobo test indexes
eco               Obo        OK  OK  OK  
edam              Obo        OK  OK  OK  
go                Obo        OK  OK  OK  
pw                Obo        OK  OK  OK  
ro                Obo        OK  OK  OK  
so                Obo        OK  OK  OK  

The output is a simple text 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
cachedas Generates server cache file for DAS servers or for the DAS registry
cachedbfetch Generates server cache file for Dbfetch/WSDbfetch data sources
cacheebeyesearch Generates server cache file for EB-eye search domains
cacheensembl Generates server cache file for an Ensembl server
dbtell Display information about a public database
servertell Display information about a public server
showserver Displays information on configured servers

Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

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