
                                  showdb 



Function

   Displays information on the currently available databases

Description

   This writes out a simple table displaying the names, contents and
   available ways of accessing the sequence databases.

   The available ways of accessing the databases are 'ID', 'Query' and
   'All'. These refer to the way that you can search the databases to get
   entries from them, which is governed by the ways the database has been
   set up and the way it is organised and indexed.

   Different databases may have different access capabilities, depending
   on how your local site is organised.

   EMBOSS has been designed to be extremely flexible in its use of
   sequence databases formats, so that it is easy to set EMBOSS up to use
   your site's existing databases. Sometimes this means that it is hard
   to extract entries from some databases in particular ways. For
   example, a flat file database with no index is only useful for reading
   all entries, while a database located in another site that is
   available via the WWW may only provide single entries.

   'ID' (also known as 'single entry') allows the programs to extract a
   single explicitly named entry from the database, for example
   embl:x13776

   'Query' (also known as 'wild') indicates that programs can extract a
   set of matching wildcard entry names (this may be slow for some
   methods of access). For example you can look at all of the human PAX
   proteins in SWISS_PROT by: swissprot:pax*_human

   'All' allows the programs to analyse all the entries in the database
   sequentially. For example this lets you look at all entries in the
   database with the notation: embl:*

   A database may have several different methods of access available.
   Ideally all of the databases available on your site will be available
   in all three ways, but this is not the best of all posssible worlds
   and so you might like to check how you can access the databases by
   running this program and having a look.

Usage

   Here is a sample session with showdb

   Display information on the currently available databases:


% showdb 
Displays information on the currently available databases

# Name           Type  ID  Qry All Comment
# ============== ==== ==  === === =======
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 inde
x
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMB
L CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM in
dex
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 ind
ex

   Example 2

   Write the results to a file:


% showdb -outfile showdb.out 
Displays information on the currently available databases

   Go to the output files for this example

   Example 3

   Display information on one explicit database:


% showdb -database tsw 
Displays information on the currently available 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 the currently available databases


 Name Type ID Qry All Comment

 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 0
2

 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

 twp P OK   OK   OK   EMBL new 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 5

   Display protein databases only:


% showdb -nonucleic 
Displays information on the currently available databases

# Name           Type  ID  Qry All Comment
# ============== ==== ==  === === =======
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 inde
x
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMB
L CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM in
dex

   Example 6

   Display the information with no headings:


% showdb -noheading 
Displays information on the currently available databases

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 inde
x
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMB
L CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM in
dex
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 ind
ex

   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
twp
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 the currently available databases

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
twp              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 the currently available databases

# Name           Type  ID  Qry All Method    Fields            Defined  Release
  Comment
# ============== ==== ==  === === ========= ================= ======= ======= =
======
qapblast         P    OK  OK  OK  blast     -                 special         B
LAST swissnew
qapblastall      P    OK  OK  OK  blast     sv,des            special         B
LAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  blast     -                 special         B
LAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  blast     -                 special         B
LAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  blast     -                 special         B
LAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  emblcd    -                 special         F
ASTA file swissnew entries
qapflat          P    OK  OK  OK  emblcd    -                 special         S
pTrEmbl flatfile
qapflatall       P    OK  OK  OK  emblcd    sv,des,org,key    special         S
pTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  gcg       -                 special         P
IR
qapirall         P    OK  OK  OK  gcg       des,org,key       special         P
IR
qapirinc         P    OK  OK  OK  gcg       -                 special         P
IR
qapxfasta        P    OK  OK  OK  emboss    -                 special         F
ASTA file swissnew entries
qapxflat         P    OK  OK  OK  emboss    -                 special         S
wissnew flatfiles
qaxpir           P    OK  OK  OK  embossgcg -                 special         P
IR
qaxpirall        P    OK  OK  OK  embossgcg des,org,key       special         P
IR
qaxpirinc        P    OK  OK  OK  embossgcg -                 special         P
IR
tpir             P    OK  OK  OK  gcg       des,org,key       special         P
IR using NBRF access for 4 files
tsw              P    OK  OK  OK  emblcd    sv,des,org,key    special 36      S
wissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  emblcd    sv,des,org,key    special 37      S
pTrEmbl as 3 files in native format with EMBL CD-ROM index
twp              P    OK  OK  OK  emblcd    des               special 16      E
MBL new in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   srswww    gi,sv,des,org,key global          G
enbank IDs
qanfasta         N    OK  OK  OK  emblcd    -                 special         F
ASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  emblcd    sv,des            special         F
ASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  emblcd    -                 special         E
MBL flatfiles
qanflatall       N    OK  OK  OK  emblcd    -                 special         E
MBL flatfiles
qanflatexc       N    OK  OK  OK  emblcd    -                 special         E
MBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  emblcd    -                 special         E
MBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  gcg       -                 special         G
CG format EMBL
qangcgall        N    OK  OK  OK  gcg       sv,des,org,key    special         G
CG format EMBL
qangcgexc        N    OK  OK  OK  gcg       -                 special         G
CG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  gcg       -                 special         G
CG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  emboss    -                 special         F
ASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  emboss    sv,des            special         F
ASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  emboss    -                 special         E
MBL flatfiles
qanxflatall      N    OK  OK  OK  emboss    des,org,key       special         E
MBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  emboss    -                 special         E
MBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  emboss    -                 special         E
MBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  embossgcg -                 special         G
CG format EMBL
qanxgcgall       N    OK  OK  OK  embossgcg sv,des,org,key    special         G
CG format EMBL
qanxgcgexc       N    OK  OK  OK  embossgcg -                 special         G
CG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  embossgcg -                 special         G
CG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  gcg       -                 special         P
IR
qasrswww         N    OK  -   -   srswww    sv,des,org,key    special         R
emote SRS web server
qawfasta         N    OK  OK  OK  emblcd    -                 special         F
ASTA file wormpep entries
qawxfasta        N    OK  OK  OK  emboss    -                 special         F
ASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  embossgcg -                 special         P
IR
tembl            N    OK  OK  OK  emblcd    sv,des,org,key    special 57      E
MBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  direct    sv,des,org,key    special 57      E
MBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  direct    sv,des,org,key    special 57      E
MBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  direct    sv,des,org,key    special 57      E
MBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  emblcd    des               special 01      t
est sequence data
tgb              N    OK  -   -   srswww    sv,des,org,key    special         G
enbank IDs
tgenbank         N    OK  OK  OK  emblcd    sv,des,org,key    special 01      G
enBank 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 standard output
   -filter             boolean    Read standard input, write 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

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
# ============== ==== ==  === === =======
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 inde
x
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMB
L CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM in
dex
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 ind
ex

   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

   Note that 'OK' in the output 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.

   You can set up your own private databases by editing a file called
   '.embossrc' to contain database specifications.

   You can set up public databases by editing the file
   '/usr/local/share/EMBOSS/emboss.default' (if you have the permission
   to do this).

   The 'emboss.default' file will already have the definitions of the
   test databases in: tsw, tembl, tpir, etc. These are the databases that
   are used in the examples shown in the documentation of the programs.

   For details of the database definitions, you should first read David's
   Administration Guide: http://emboss.sourceforge.net/docs/adminguide/
   especially:
   http://emboss.sourceforge.net/docs/adminguide/adminguide/node4.html 

   See also: http://emboss.sourceforge.net/docs/themes/Databases.html for
   a lot of detail of the syntax of database definition.

   Just because showdb can display the database definitions, it does NOT
   mean that the databases are set up correctly. You must now test them
   using seqret.

References

   None.

Warnings

   None.

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      Reads ABI file and display the trace
   cirdna       Draws circular maps of DNA constructs
   infoalign    Information on a multiple sequence alignment
   infoseq      Displays some simple information about sequences
   lindna       Draws linear maps of DNA constructs
   pepnet       Displays proteins as a helical net
   pepwheel     Shows protein sequences as helices
   prettyplot   Displays aligned sequences, with colouring and boxing
   prettyseq    Output sequence with translated ranges
   remap        Display sequence with restriction sites, translation etc
   seealso      Finds programs sharing group names
   showalign    Displays a multiple sequence alignment
   showfeat     Show features of a sequence
   showseq      Display a sequence with features, translation etc
   sixpack      Display a DNA sequence with 6-frame translation and ORFs
   textsearch   Search sequence documentation. Slow, use SRS and Entrez!
   tfm          Displays a program's help documentation manual
   whichdb      Search all databases for an entry
   wossname     Finds programs by keywords in their one-line documentation

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
