                                   showdb



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   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
# ============== ========== ==  === === =======
twp              Protein    OK  OK  OK  EMBL new in native format with EMBL CD-R
OM index
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 fil
e 02
qapblastsplitinc Protein    OK  OK  OK  BLAST swissnew split in 5 files, only fi
le 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 wit
h EMBL CD-ROM index
genbanksrs       Nucleotide OK  OK  OK  Genbank IDs
qanfasta         Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanfastaall      Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields inde
xed
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 inde
xed
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 i
ndex
temblall         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM i
ndex
temblrest        Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM i
ndex
temblvrt         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM i
ndex
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-RO
M 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            Protein OK  OK  OK  Swissprot native format with EMBL CD-ROM inde
x


   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


 Name Type ID Qry All Comment

 twp Protein OK   OK   OK   EMBL new in native format with EMBL CD-ROM index

 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 fi
le 02

 qapblastsplitinc Protein OK   OK   OK   BLAST swissnew split in 5 files, only f
ile 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

 genbanksrs Nucleotide OK   OK   OK   Genbank IDs

 qanfasta Nucleotide OK   OK   OK   FASTA file EMBL rodents

 qanfastaall Nucleotide OK   OK   OK   FASTA file EMBL rodents, all fields index
ed

 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 inde
xed

 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 inde
x

 temblvrt Nucleotide OK   OK   OK   EMBL in native format with EMBL CD-ROM index

 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 in
dex




   Example 5

   Display protein databases only:


% showdb -nonucleic
Displays information on configured databases

# Name           Type       ID  Qry All Comment
# ============== ========== ==  === === =======
twp              Protein    OK  OK  OK  EMBL new in native format with EMBL CD-R
OM index
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 fil
e 02
qapblastsplitinc Protein    OK  OK  OK  BLAST swissnew split in 5 files, only fi
le 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 wit
h EMBL CD-ROM index


   Example 6

   Display the information with no headings:


% showdb -noheading
Displays information on configured databases

twp              Protein    OK  OK  OK  EMBL new in native format with EMBL CD-R
OM index
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 fil
e 02
qapblastsplitinc Protein    OK  OK  OK  BLAST swissnew split in 5 files, only fi
le 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 wit
h EMBL CD-ROM index
genbanksrs       Nucleotide OK  OK  OK  Genbank IDs
qanfasta         Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanfastaall      Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields inde
xed
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 inde
xed
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 i
ndex
temblall         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM i
ndex
temblrest        Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM i
ndex
temblvrt         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM i
ndex
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-RO
M 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              Protein
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
genbanksrs       Nucleotide
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
testdb           Nucleotide
tgb              Nucleotide
tgenbank         Nucleotide


   Example 9

   Display everything


% showdb -full
Displays information on configured databases

# Name           Type       ID  Qry All Method    Fields            Defined Rele
ase Comment
# ============== ========== ==  === === ========= ================= ======= ====
=== =======
twp              Protein    OK  OK  OK  emblcd    des               global  16
    EMBL new in native format with EMBL CD-ROM index
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    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
genbanksrs       Nucleotide OK  OK  OK  srswww    gi,sv,des,org,key global
    Genbank IDs
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
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


Command line arguments

Displays information on configured databases
Version: EMBOSS:6.3.0

   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 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 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


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              Protein    OK  OK  OK  EMBL new in native format with EMBL CD-R
OM index
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 fil
e 02
qapblastsplitinc Protein    OK  OK  OK  BLAST swissnew split in 5 files, only fi
le 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 wit
h EMBL CD-ROM index
genbanksrs       Nucleotide OK  OK  OK  Genbank IDs
qanfasta         Nucleotide OK  OK  OK  FASTA file EMBL rodents
qanfastaall      Nucleotide OK  OK  OK  FASTA file EMBL rodents, all fields inde
xed
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 inde
xed
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 i
ndex
temblall         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM i
ndex
temblrest        Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM i
ndex
temblvrt         Nucleotide OK  OK  OK  EMBL in native format with EMBL CD-ROM i
ndex
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-RO
M 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 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 (c) 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
