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showdb |
Wiki
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Function
Display information on configured databasesDescription
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 showdbDisplay information on the currently available databases:
% showdb Display information on configured databases # Name Type Comment # =============== ============================= ======= bpsw Protein,Protfeatures BioPerl OBDA index of test SwissProt bpworm Protein BioPerl OBDA index of test wormpep fasta file qapblast Protein BLAST swissnew qapblastall Protein BLAST swissnew, all fields indexed qapblastsplit Protein BLAST swissnew split in 5 files qapblastsplitexc Protein BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein BLAST swissnew split in 5 files, only file 02 qapfasta Protein FASTA file swissnew entries qapflat Protein,Protfeatures SpTrEmbl flatfile qapflatall Protein,Protfeatures SpTrEmbl flatfiles, all fields indexed qapir Protein,Protfeatures Test PIR indexed by dbigcg qapirall Protein,Protfeatures Test PIR indexed by dbigcg with fields qapirexc Protein,Protfeatures Test PIR indexed by dbigcg except file pir1 qapirinc Protein,Protfeatures Test PIR indexed by dbigcg file pir1 qapxfasta Protein FASTA file swissnew entries qapxflat Protein Swissnew flatfiles qasrswww Protein,Protfeatures Remote SRS web server qaxpir Protein,Protfeatures PIR indexed by dbxgcg qaxpirall Protein,Protfeatures Test PIR indexed by dbxgcg with fields qaxpirexc Protein,Protfeatures Test PIR indexed by dbxgcg except pir1 qaxpirinc Protein,Protfeatures Test PIR indexed by dbxgcg file pir1 tpir Protein Test PIR using NBRF access for 4 files tsw Protein,Protfeatures,Text Swissprot native format with EMBL CD-ROM index tswnew Protein,Protfeatures SpTrEmbl as 3 files in native format with EMBL CD-ROM index bpembl Nucleotide,Nucfeatures BioPerl OBDA index of test EMBL bpgb Nucleotide,Nucfeatures BioPerl OBDA index of test GenBank ena Nucleotide,Nucfeatures ENA via URL qanfasta Nucleotide FASTA file EMBL rodents qanfastaall Nucleotide FASTA file EMBL rodents, all fields indexed qanflat Nucleotide,Nucfeatures,Refseq EMBL flatfiles qanflatall Nucleotide,Nucfeatures,Refseq EMBL flatfiles qanflatexc Nucleotide,Nucfeatures EMBL flatfiles, no rodent file qanflatinc Nucleotide,Nucfeatures EMBL flatfiles, only rodent file qangcg Nucleotide,Nucfeatures GCG format test EMBL qangcgall Nucleotide,Nucfeatures GCG format test EMBL qangcgexc Nucleotide,Nucfeatures GCG format test EMBL without prokaryotes qangcginc Nucleotide,Nucfeatures GCG format test EMBL only prokaryotes qanxfasta Nucleotide FASTA file EMBL rodents qanxfastaall Nucleotide FASTA file EMBL rodents, all fields indexed qanxflat Nucleotide,Nucfeatures,Refseq EMBL flatfiles qanxflatall Nucleotide,Nucfeatures,Refseq EMBL flatfiles, all fields indexed qanxflatexc Nucleotide,Nucfeatures,Refseq EMBL flatfiles, no rodent file qanxflatinc Nucleotide,Nucfeatures EMBL flatfiles, only rodent file qanxgcg Nucleotide,Nucfeatures GCG format EMBL qanxgcgall Nucleotide,Nucfeatures GCG format EMBL indexed by dbxgcg with query fields qanxgcgexc Nucleotide,Nucfeatures GCG format EMBL without prokaryotes qanxgcginc Nucleotide,Nucfeatures GCG format EMBL only prokaryotes qawfasta Nucleotide FASTA file wormpep entries qawxfasta Nucleotide FASTA file wormpep entries qaxembl Nucleotide,Nucfeatures,Refseq EMBL flatfiles tembl Nucleotide,Refseq,Nucfeatures EMBL in native format with EMBL CD-ROM index temblall Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index temblrest Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index temblvrt Nucleotide,Nucfeatures EMBL in native format with EMBL CD-ROM index tensembldasgrch37 Nucleotide Homo_sapiens Reference server based on GRCh37 assembly testdb Nucleotide test sequence data tgb Nucleotide,Nucfeatures Genbank by SRS at DKFZ tgenbank Nucleotide,Nucfeatures Test GenBank in native format with EMBL CD-ROM index tgenedashuman Nucleotide The Ensembl human Gene_ID reference source tflybase Features Flybase CHADO server tgenedb Features GeneDb CHADO server ttax Taxonomy NCBI taxonomy test data taxon Taxonomy NCBI taxonomy drcat Resource Data Resource Catalogue tedam Obo Test EDAM using dbxedam test indexes tobo Obo Test EDAM using dbxobo test indexes chebi Obo Chemical Entities of Biological Interest eco Obo Evidence code ontology edam Obo EMBRACE Data and Methods ontology edam_data Obo EMBRACE Data and Methods ontology (data) edam_format Obo EMBRACE Data and Methods ontology (formats) edam_identifier Obo EMBRACE Data and Methods ontology (identifiers) edam_operation Obo EMBRACE Data and Methods ontology (operations) edam_topic Obo EMBRACE Data and Methods ontology (topics) go Obo Gene Ontology go_component Obo Gene Ontology (cellular components) go_function Obo Gene Ontology (molecular functions) go_process Obo Gene Ontology (biological processes) pw Obo Pathways ontology ro Obo Relations ontology so Obo Sequence ontology swo Obo Software ontology |
Example 2
Write the results to a file:
% showdb -outfile showdb.out Display information on configured databases |
Go to the output files for this example
Example 3
Display information on one explicit database:
% showdb -database tsw Display information on configured databases # Name Type Comment # ============ ========================= ======= tsw Protein,Protfeatures,Text 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 Display information on configured databases
|
Example 5
Display protein databases only:
% showdb -nonucleic Display information on configured databases # Name Type Comment # =============== ============================= ======= bpsw Protein,Protfeatures BioPerl OBDA index of test SwissProt bpworm Protein BioPerl OBDA index of test wormpep fasta file qapblast Protein BLAST swissnew qapblastall Protein BLAST swissnew, all fields indexed qapblastsplit Protein BLAST swissnew split in 5 files qapblastsplitexc Protein BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein BLAST swissnew split in 5 files, only file 02 qapfasta Protein FASTA file swissnew entries qapflat Protein,Protfeatures SpTrEmbl flatfile qapflatall Protein,Protfeatures SpTrEmbl flatfiles, all fields indexed qapir Protein,Protfeatures Test PIR indexed by dbigcg qapirall Protein,Protfeatures Test PIR indexed by dbigcg with fields qapirexc Protein,Protfeatures Test PIR indexed by dbigcg except file pir1 qapirinc Protein,Protfeatures Test PIR indexed by dbigcg file pir1 qapxfasta Protein FASTA file swissnew entries qapxflat Protein Swissnew flatfiles qasrswww Protein,Protfeatures Remote SRS web server qaxpir Protein,Protfeatures PIR indexed by dbxgcg qaxpirall Protein,Protfeatures Test PIR indexed by dbxgcg with fields qaxpirexc Protein,Protfeatures Test PIR indexed by dbxgcg except pir1 qaxpirinc Protein,Protfeatures Test PIR indexed by dbxgcg file pir1 tpir Protein Test PIR using NBRF access for 4 files tsw Protein,Protfeatures,Text Swissprot native format with EMBL CD-ROM index tswnew Protein,Protfeatures SpTrEmbl as 3 files in native format with EMBL CD-ROM index tflybase Features Flybase CHADO server tgenedb Features GeneDb CHADO server ttax Taxonomy NCBI taxonomy test data taxon Taxonomy NCBI taxonomy drcat Resource Data Resource Catalogue tedam Obo Test EDAM using dbxedam test indexes tobo Obo Test EDAM using dbxobo test indexes chebi Obo Chemical Entities of Biological Interest eco Obo Evidence code ontology edam Obo EMBRACE Data and Methods ontology edam_data Obo EMBRACE Data and Methods ontology (data) edam_format Obo EMBRACE Data and Methods ontology (formats) edam_identifier Obo EMBRACE Data and Methods ontology (identifiers) edam_operation Obo EMBRACE Data and Methods ontology (operations) edam_topic Obo EMBRACE Data and Methods ontology (topics) go Obo Gene Ontology go_component Obo Gene Ontology (cellular components) go_function Obo Gene Ontology (molecular functions) go_process Obo Gene Ontology (biological processes) pw Obo Pathways ontology ro Obo Relations ontology so Obo Sequence ontology swo Obo Software ontology |
Example 6
Display the information with no headings:
% showdb -noheading Display information on configured databases bpsw Protein,Protfeatures BioPerl OBDA index of test SwissProt bpworm Protein BioPerl OBDA index of test wormpep fasta file qapblast Protein BLAST swissnew qapblastall Protein BLAST swissnew, all fields indexed qapblastsplit Protein BLAST swissnew split in 5 files qapblastsplitexc Protein BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein BLAST swissnew split in 5 files, only file 02 qapfasta Protein FASTA file swissnew entries qapflat Protein,Protfeatures SpTrEmbl flatfile qapflatall Protein,Protfeatures SpTrEmbl flatfiles, all fields indexed qapir Protein,Protfeatures Test PIR indexed by dbigcg qapirall Protein,Protfeatures Test PIR indexed by dbigcg with fields qapirexc Protein,Protfeatures Test PIR indexed by dbigcg except file pir1 qapirinc Protein,Protfeatures Test PIR indexed by dbigcg file pir1 qapxfasta Protein FASTA file swissnew entries qapxflat Protein Swissnew flatfiles qasrswww Protein,Protfeatures Remote SRS web server qaxpir Protein,Protfeatures PIR indexed by dbxgcg qaxpirall Protein,Protfeatures Test PIR indexed by dbxgcg with fields qaxpirexc Protein,Protfeatures Test PIR indexed by dbxgcg except pir1 qaxpirinc Protein,Protfeatures Test PIR indexed by dbxgcg file pir1 tpir Protein Test PIR using NBRF access for 4 files tsw Protein,Protfeatures,Text Swissprot native format with EMBL CD-ROM index tswnew Protein,Protfeatures SpTrEmbl as 3 files in native format with EMBL CD-ROM index bpembl Nucleotide,Nucfeatures BioPerl OBDA index of test EMBL bpgb Nucleotide,Nucfeatures BioPerl OBDA index of test GenBank ena Nucleotide,Nucfeatures ENA via URL qanfasta Nucleotide FASTA file EMBL rodents qanfastaall Nucleotide FASTA file EMBL rodents, all fields indexed qanflat Nucleotide,Nucfeatures,Refseq EMBL flatfiles qanflatall Nucleotide,Nucfeatures,Refseq EMBL flatfiles qanflatexc Nucleotide,Nucfeatures EMBL flatfiles, no rodent file qanflatinc Nucleotide,Nucfeatures EMBL flatfiles, only rodent file qangcg Nucleotide,Nucfeatures GCG format test EMBL qangcgall Nucleotide,Nucfeatures GCG format test EMBL qangcgexc Nucleotide,Nucfeatures GCG format test EMBL without prokaryotes qangcginc Nucleotide,Nucfeatures GCG format test EMBL only prokaryotes qanxfasta Nucleotide FASTA file EMBL rodents qanxfastaall Nucleotide FASTA file EMBL rodents, all fields indexed qanxflat Nucleotide,Nucfeatures,Refseq EMBL flatfiles qanxflatall Nucleotide,Nucfeatures,Refseq EMBL flatfiles, all fields indexed qanxflatexc Nucleotide,Nucfeatures,Refseq EMBL flatfiles, no rodent file qanxflatinc Nucleotide,Nucfeatures EMBL flatfiles, only rodent file qanxgcg Nucleotide,Nucfeatures GCG format EMBL qanxgcgall Nucleotide,Nucfeatures GCG format EMBL indexed by dbxgcg with query fields qanxgcgexc Nucleotide,Nucfeatures GCG format EMBL without prokaryotes qanxgcginc Nucleotide,Nucfeatures GCG format EMBL only prokaryotes qawfasta Nucleotide FASTA file wormpep entries qawxfasta Nucleotide FASTA file wormpep entries qaxembl Nucleotide,Nucfeatures,Refseq EMBL flatfiles tembl Nucleotide,Refseq,Nucfeatures EMBL in native format with EMBL CD-ROM index temblall Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index temblrest Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index temblvrt Nucleotide,Nucfeatures EMBL in native format with EMBL CD-ROM index tensembldasgrch37 Nucleotide Homo_sapiens Reference server based on GRCh37 assembly testdb Nucleotide test sequence data tgb Nucleotide,Nucfeatures Genbank by SRS at DKFZ tgenbank Nucleotide,Nucfeatures Test GenBank in native format with EMBL CD-ROM index tgenedashuman Nucleotide The Ensembl human Gene_ID reference source tflybase Features Flybase CHADO server tgenedb Features GeneDb CHADO server ttax Taxonomy NCBI taxonomy test data taxon Taxonomy NCBI taxonomy drcat Resource Data Resource Catalogue tedam Obo Test EDAM using dbxedam test indexes tobo Obo Test EDAM using dbxobo test indexes chebi Obo Chemical Entities of Biological Interest eco Obo Evidence code ontology edam Obo EMBRACE Data and Methods ontology edam_data Obo EMBRACE Data and Methods ontology (data) edam_format Obo EMBRACE Data and Methods ontology (formats) edam_identifier Obo EMBRACE Data and Methods ontology (identifiers) edam_operation Obo EMBRACE Data and Methods ontology (operations) edam_topic Obo EMBRACE Data and Methods ontology (topics) go Obo Gene Ontology go_component Obo Gene Ontology (cellular components) go_function Obo Gene Ontology (molecular functions) go_process Obo Gene Ontology (biological processes) pw Obo Pathways ontology ro Obo Relations ontology so Obo Sequence ontology swo Obo Software ontology |
Example 7
Display just a list of the available database names:
% showdb -noheading -notype -noid -noquery -noall -nocomment -auto bpsw bpworm qapblast qapblastall qapblastsplit qapblastsplitexc qapblastsplitinc qapfasta qapflat qapflatall qapir qapirall qapirexc qapirinc qapxfasta qapxflat qasrswww qaxpir qaxpirall qaxpirexc qaxpirinc tpir tsw tswnew bpembl bpgb ena qanfasta qanfastaall qanflat qanflatall qanflatexc qanflatinc qangcg qangcgall qangcgexc qangcginc qanxfasta qanxfastaall qanxflat qanxflatall qanxflatexc qanxflatinc qanxgcg qanxgcgall qanxgcgexc qanxgcginc qawfasta qawxfasta qaxembl tembl temblall temblrest temblvrt tensembldasgrch37 testdb tgb tgenbank tgenedashuman tflybase tgenedb ttax taxon drcat tedam tobo chebi eco edam edam_data edam_format edam_identifier edam_operation edam_topic go go_component go_function go_process pw ro so swo |
Example 8
Display only the names and types:
% showdb -only -type Display information on configured databases bpsw Protein,Protfeatures bpworm Protein qapblast Protein qapblastall Protein qapblastsplit Protein qapblastsplitexc Protein qapblastsplitinc Protein qapfasta Protein qapflat Protein,Protfeatures qapflatall Protein,Protfeatures qapir Protein,Protfeatures qapirall Protein,Protfeatures qapirexc Protein,Protfeatures qapirinc Protein,Protfeatures qapxfasta Protein qapxflat Protein qasrswww Protein,Protfeatures qaxpir Protein,Protfeatures qaxpirall Protein,Protfeatures qaxpirexc Protein,Protfeatures qaxpirinc Protein,Protfeatures tpir Protein tsw Protein,Protfeatures,Text tswnew Protein,Protfeatures bpembl Nucleotide,Nucfeatures bpgb Nucleotide,Nucfeatures ena Nucleotide,Nucfeatures qanfasta Nucleotide qanfastaall Nucleotide qanflat Nucleotide,Nucfeatures,Refseq qanflatall Nucleotide,Nucfeatures,Refseq qanflatexc Nucleotide,Nucfeatures qanflatinc Nucleotide,Nucfeatures qangcg Nucleotide,Nucfeatures qangcgall Nucleotide,Nucfeatures qangcgexc Nucleotide,Nucfeatures qangcginc Nucleotide,Nucfeatures qanxfasta Nucleotide qanxfastaall Nucleotide qanxflat Nucleotide,Nucfeatures,Refseq qanxflatall Nucleotide,Nucfeatures,Refseq qanxflatexc Nucleotide,Nucfeatures,Refseq qanxflatinc Nucleotide,Nucfeatures qanxgcg Nucleotide,Nucfeatures qanxgcgall Nucleotide,Nucfeatures qanxgcgexc Nucleotide,Nucfeatures qanxgcginc Nucleotide,Nucfeatures qawfasta Nucleotide qawxfasta Nucleotide qaxembl Nucleotide,Nucfeatures,Refseq tembl Nucleotide,Refseq,Nucfeatures temblall Nucleotide,Nucfeatures,Refseq temblrest Nucleotide,Nucfeatures,Refseq temblvrt Nucleotide,Nucfeatures tensembldasgrch37 Nucleotide testdb Nucleotide tgb Nucleotide,Nucfeatures tgenbank Nucleotide,Nucfeatures tgenedashuman Nucleotide tflybase Features tgenedb Features ttax Taxonomy taxon Taxonomy drcat Resource tedam Obo tobo Obo chebi Obo eco Obo edam Obo edam_data Obo edam_format Obo edam_identifier Obo edam_operation Obo edam_topic Obo go Obo go_component Obo go_function Obo go_process Obo pw Obo ro Obo so Obo swo Obo |
Example 9
Display everything
% showdb -full Display information on configured databases # Name Type ID Qry All Method Taxon Fields Aliases Examples Defined Release Comment # =============== ============================= == === === ========= =========================== ===================================================================================================== =============== ================== ======== =================== ======= bpsw Protein,Protfeatures OK OK OK obda - 2 id,acc 0 - 0 - special BioPerl OBDA index of test SwissProt bpworm Protein OK OK OK obda - 1 id 0 - 0 - special BioPerl OBDA index of test wormpep fasta file qapblast Protein OK OK OK blast 1_all 2 id,acc 0 - 0 - special BLAST swissnew qapblastall Protein OK OK OK blast 1_all 4 sv,des 0 - 0 - special BLAST swissnew, all fields indexed qapblastsplit Protein OK OK OK blast 1_all 2 id,acc 0 - 0 - special BLAST swissnew split in 5 files qapblastsplitexc Protein OK OK OK blast 1_all 2 id,acc 0 - 0 - special BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein OK OK OK blast 1_all 2 id,acc 0 - 0 - special BLAST swissnew split in 5 files, only file 02 qapfasta Protein OK OK OK emblcd 1_all 2 id,acc 0 - 0 - special FASTA file swissnew entries qapflat Protein,Protfeatures OK OK OK emblcd 1_all 2 id,acc 0 - 0 - special SpTrEmbl flatfile qapflatall Protein,Protfeatures OK OK OK emblcd 1_all 6 sv,des,org,key 0 - 0 - special SpTrEmbl flatfiles, all fields indexed qapir Protein,Protfeatures OK OK OK gcg 1_all 2 id,acc 0 - 0 - special Test PIR indexed by dbigcg qapirall Protein,Protfeatures OK OK OK gcg 1_all 5 des,org,key 0 - 0 - special Test PIR indexed by dbigcg with fields qapirexc Protein,Protfeatures OK OK OK gcg 1_all 2 id,acc 0 - 0 - special Test PIR indexed by dbigcg except file pir1 qapirinc Protein,Protfeatures OK OK OK gcg 1_all 2 id,acc 0 - 0 - special Test PIR indexed by dbigcg file pir1 qapxfasta Protein OK OK OK emboss 1_all 2 id,acc 0 - 0 - special FASTA file swissnew entries qapxflat Protein OK OK OK emboss 1_all 2 id,acc 0 - 0 - special Swissnew flatfiles qasrswww Protein,Protfeatures OK OK OK srswww 1_all 6 sv,des,org,key 0 - 0 - special Remote SRS web server qaxpir Protein,Protfeatures OK OK OK embossgcg 1_all 2 id,acc 0 - 0 - special PIR indexed by dbxgcg qaxpirall Protein,Protfeatures OK OK OK embossgcg 1_all 5 des,org,key 0 - 0 - special Test PIR indexed by dbxgcg with fields qaxpirexc Protein,Protfeatures OK OK OK embossgcg 1_all 2 id,acc 0 - 0 - special Test PIR indexed by dbxgcg except pir1 qaxpirinc Protein,Protfeatures OK OK OK embossgcg 1_all 2 id,acc 0 - 0 - special Test PIR indexed by dbxgcg file pir1 tpir Protein OK OK OK gcg 1_all 5 des,org,key 0 - 0 - special Test PIR using NBRF access for 4 files tsw Protein,Protfeatures,Text OK OK OK emblcd 1_all 6 id,acc,sv,des,org,key 0 - 1 hba_human special 36 Swissprot native format with EMBL CD-ROM index tswnew Protein,Protfeatures OK OK OK emblcd 1_all 6 sv,des,org,key 0 - 0 - special 37 SpTrEmbl as 3 files in native format with EMBL CD-ROM index bpembl Nucleotide,Nucfeatures OK OK OK obda - 2 id,acc 0 - 0 - special BioPerl OBDA index of test EMBL bpgb Nucleotide,Nucfeatures OK OK OK obda - 2 id,acc 0 - 0 - special BioPerl OBDA index of test GenBank ena Nucleotide,Nucfeatures OK OK OK url 1_all 2 id,acc 0 - 0 - special ENA via URL qanfasta Nucleotide OK OK OK emblcd 9989_rodentia 2 id,acc 0 - 0 - special FASTA file EMBL rodents qanfastaall Nucleotide OK OK OK emblcd 9989_rodentia 4 sv,des 0 - 0 - special FASTA file EMBL rodents, all fields indexed qanflat Nucleotide,Nucfeatures,Refseq OK OK OK emblcd 1_all 2 id,acc 0 - 0 - special EMBL flatfiles qanflatall Nucleotide,Nucfeatures,Refseq OK OK OK emblcd 1_all 2 id,acc 0 - 0 - special EMBL flatfiles qanflatexc Nucleotide,Nucfeatures OK OK OK emblcd 1_all 2 id,acc 0 - 0 - special EMBL flatfiles, no rodent file qanflatinc Nucleotide,Nucfeatures OK OK OK emblcd - 2 id,acc 0 - 0 - special EMBL flatfiles, only rodent file qangcg Nucleotide,Nucfeatures OK OK OK gcg 1_all 2 id,acc 0 - 0 - special GCG format test EMBL qangcgall Nucleotide,Nucfeatures OK OK OK gcg 1_all 6 sv,des,org,key 0 - 0 - special GCG format test EMBL qangcgexc Nucleotide,Nucfeatures OK OK OK gcg 1_all 2 id,acc 0 - 0 - special GCG format test EMBL without prokaryotes qangcginc Nucleotide,Nucfeatures OK OK OK gcg 1_all 2 id,acc 0 - 0 - special GCG format test EMBL only prokaryotes qanxfasta Nucleotide OK OK OK emboss 9989_rodentia 2 id,acc 0 - 0 - special FASTA file EMBL rodents qanxfastaall Nucleotide OK OK OK emboss 9989_rodentia 4 sv,des 0 - 0 - special FASTA file EMBL rodents, all fields indexed qanxflat Nucleotide,Nucfeatures,Refseq OK OK OK emboss 1_all 2 id,acc 0 - 0 - special EMBL flatfiles qanxflatall Nucleotide,Nucfeatures,Refseq OK OK OK emboss 1_all 6 des,org,key,sv 0 - 0 - special EMBL flatfiles, all fields indexed qanxflatexc Nucleotide,Nucfeatures,Refseq OK OK OK emboss 1_all 2 id,acc 0 - 0 - special EMBL flatfiles, no rodent file qanxflatinc Nucleotide,Nucfeatures OK OK OK emboss 1_all 2 id,acc 0 - 0 - special EMBL flatfiles, only rodent file qanxgcg Nucleotide,Nucfeatures OK OK OK embossgcg 1_all 2 id,acc 0 - 0 - special GCG format EMBL qanxgcgall Nucleotide,Nucfeatures OK OK OK embossgcg 1_all 6 sv,des,org,key 0 - 0 - special GCG format EMBL indexed by dbxgcg with query fields qanxgcgexc Nucleotide,Nucfeatures OK OK OK embossgcg 1_all 2 id,acc 0 - 0 - special GCG format EMBL without prokaryotes qanxgcginc Nucleotide,Nucfeatures OK OK OK embossgcg 1_all 2 id,acc 0 - 0 - special GCG format EMBL only prokaryotes qawfasta Nucleotide OK OK OK emblcd 6239_caenorhabditis_elegans 2 id,acc 0 - 0 - special FASTA file wormpep entries qawxfasta Nucleotide OK OK OK emboss 6239_caenorhabditis_elegans 2 id,acc 0 - 0 - special FASTA file wormpep entries qaxembl Nucleotide,Nucfeatures,Refseq OK OK OK emboss 1_all 2 id,acc 0 - 0 - special EMBL flatfiles tembl Nucleotide,Refseq,Nucfeatures OK OK OK emblcd 1_all 6 sv,des,org,key 0 - 1 x13776 special 57 EMBL in native format with EMBL CD-ROM index temblall Nucleotide,Nucfeatures,Refseq OK OK OK direct 1_all 6 sv,des,org,key 0 - 0 - special 57 EMBL in native format with EMBL CD-ROM index temblrest Nucleotide,Nucfeatures,Refseq OK OK OK direct 1_all 6 sv,des,org,key 0 - 0 - special 57 EMBL in native format with EMBL CD-ROM index temblvrt Nucleotide,Nucfeatures OK OK OK direct 9711_chordata 6 sv,des,org,key 0 - 0 - special 57 EMBL in native format with EMBL CD-ROM index tensembldasgrch37 Nucleotide OK OK - das 9606_homo_sapiens 2 id,acc 0 - 0 - special Homo_sapiens Reference server based on GRCh37 assembly testdb Nucleotide OK OK OK emblcd - 3 des 0 - 0 - special 01 test sequence data tgb Nucleotide,Nucfeatures OK OK OK srswww 1_all 6 sv,des,org,key 0 - 0 - special Genbank by SRS at DKFZ tgenbank Nucleotide,Nucfeatures OK OK OK emblcd 1_all 6 sv,des,org,key 0 - 0 - special 01 Test GenBank in native format with EMBL CD-ROM index tgenedashuman Nucleotide OK OK - das 9606_homo_sapiens 2 id,acc 0 - 0 - special The Ensembl human Gene_ID reference source tflybase Features OK - - chado(id) 1_all 2 uniquename 0 - 0 - special Flybase CHADO server tgenedb Features OK - - chado(id) 1_all 2 uniquename 0 - 0 - special GeneDb CHADO server ttax Taxonomy OK OK OK embosstax - 7 id,acc,nam,rnk,up,gc,mgc 0 - 0 - special NCBI taxonomy test data taxon Taxonomy OK OK OK embosstax 1 7 id,acc,tax,rnk,up,gc,mgc 0 - 0 - standard July 2012 NCBI taxonomy drcat Resource OK OK OK emboss none 21 id,acc,nam,des,url,cat,edat,efmt,eid,etpc,xref,qout,qfmt,qin,qurl,cc,rest,soap,stat,xref,taxid 0 - 0 - standard alpha 1 21-jun-2011 Data Resource Catalogue tedam Obo OK OK OK emboss - 12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc 0 - 0 - special beta11 Test EDAM using dbxedam test indexes tobo Obo OK OK OK emboss - 12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc 0 - 0 - special beta11 Test EDAM using dbxobo test indexes chebi Obo OK OK OK emboss none 5 id,acc,nam,isa,des 0 - 0 - standard 93 Chemical Entities of Biological Interest eco Obo OK OK OK emboss none 5 id,acc,nam,isa,des 0 - 0 - standard 2.02 Evidence code ontology edam Obo OK OK OK emboss none 12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc 0 - 0 - standard 1.1 EMBRACE Data and Methods ontology edam_data Obo OK OK OK emboss none 12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc 0 - 0 - standard 1.1 EMBRACE Data and Methods ontology (data) edam_format Obo OK OK OK emboss none 12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc 0 - 0 - standard 1.1 EMBRACE Data and Methods ontology (formats) edam_identifier Obo OK OK OK emboss none 12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc 0 - 0 - standard 1.1 EMBRACE Data and Methods ontology (identifiers) edam_operation Obo OK OK OK emboss none 12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc 0 - 0 - standard 1.1 EMBRACE Data and Methods ontology (operations) edam_topic Obo OK OK OK emboss none 12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,issrc 0 - 0 - standard 1.1 EMBRACE Data and Methods ontology (topics) go Obo OK OK OK emboss 1_all 6 id,acc,nam,isa,des,ns 0 - 0 - standard 1.1.3300 Gene Ontology go_component Obo OK OK OK emboss 1_all 6 id,acc,nam,isa,des,ns 0 - 0 - standard 1.1.3300 Gene Ontology (cellular components) go_function Obo OK OK OK emboss 1_all 6 id,acc,nam,isa,des,ns 0 - 0 - standard 1.1.3300 Gene Ontology (molecular functions) go_process Obo OK OK OK emboss 1_all 6 id,acc,nam,isa,des,ns 0 - 0 - standard 1.1.3300 Gene Ontology (biological processes) pw Obo OK OK OK emboss 1_all 5 id,acc,nam,isa,des 0 - 0 - standard 12:06:2012 11:03 Pathways ontology ro Obo OK OK OK emboss none 5 id,acc,nam,isa,des 0 - 0 - standard 20:03:2009 11:58 Relations ontology so Obo OK OK OK emboss none 5 id,acc,nam,isa,des 0 - 0 - standard 02:05:2012 11:08 Sequence ontology swo Obo OK OK OK emboss none 5 id,acc,nam,isa,des 0 - 0 - standard 12-jul-2012 Software ontology |
Command line arguments
Display information on configured databases
Version: EMBOSS:6.6.0.0
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
-[no]xml boolean [Y] Display XML databases
-[no]standard boolean [Y] Display standard databases
-[no]user boolean [Y] Display user-defined databases
-[no]include boolean [Y] Display databases defined in included
files
-full boolean [N] Display all columns
-access boolean [$(full)] This displays the levels of access
that can be used on this database
-methods boolean [$(full)] This displays the access methods
that can be used on this database, for all,
query or ID access
-taxscope boolean [$(full)] This displays the taxons covered
by this database
-fields boolean [$(full)] This displays the search fields
that can be used on this database, including
the standard 'id' or 'acc' fields
-numfields boolean [$(full)] This displays the number of search
fields that can be used on this database,
including the standard 'id' or 'acc' fields
-aliases boolean [$(full)] This displays the alias names that
can be used for this database
-numaliases boolean [$(full)] This displays the number of alias
names that can be used for this database
-examples boolean [$(full)] This displays the example queries
that can be used to test this database
-numexamples boolean [$(full)] This displays the number of
example queries that can be used to test
this database
-defined boolean [$(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' access column
-query boolean [@(!$(only))] Display 'qry' access column
-all boolean [@(!$(only))] Display 'all' access 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 |
| -[no]xml | boolean | Display XML databases | Boolean value Yes/No | Yes |
| -[no]standard | boolean | Display standard databases | Boolean value Yes/No | Yes |
| -[no]user | boolean | Display user-defined databases | Boolean value Yes/No | Yes |
| -[no]include | boolean | Display databases defined in included files | Boolean value Yes/No | Yes |
| -full | boolean | Display all columns | Boolean value Yes/No | No |
| -access | boolean | This displays the levels of access that can be used on this database | Boolean value Yes/No | $(full) |
| -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) |
| -taxscope | boolean | This displays the taxons covered by this database | Boolean value Yes/No | $(full) |
| -fields | boolean | This displays the search fields that can be used on this database, including the standard 'id' or 'acc' fields | Boolean value Yes/No | $(full) |
| -numfields | boolean | This displays the number of search fields that can be used on this database, including the standard 'id' or 'acc' fields | Boolean value Yes/No | $(full) |
| -aliases | boolean | This displays the alias names that can be used for this database | Boolean value Yes/No | $(full) |
| -numaliases | boolean | This displays the number of alias names that can be used for this database | Boolean value Yes/No | $(full) |
| -examples | boolean | This displays the example queries that can be used to test this database | Boolean value Yes/No | $(full) |
| -numexamples | boolean | This displays the number of example queries that can be used to test this database | 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 | @(!$(only)) |
| -id | boolean | Display 'id' access column | Boolean value Yes/No | @(!$(only)) |
| -query | boolean | Display 'qry' access column | Boolean value Yes/No | @(!$(only)) |
| -all | boolean | Display 'all' access column | Boolean value Yes/No | @(!$(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 Comment # =============== ============================= ======= bpsw Protein,Protfeatures BioPerl OBDA index of test SwissProt bpworm Protein BioPerl OBDA index of test wormpep fasta file qapblast Protein BLAST swissnew qapblastall Protein BLAST swissnew, all fields indexed qapblastsplit Protein BLAST swissnew split in 5 files qapblastsplitexc Protein BLAST swissnew split in 5 files, not file 02 qapblastsplitinc Protein BLAST swissnew split in 5 files, only file 02 qapfasta Protein FASTA file swissnew entries qapflat Protein,Protfeatures SpTrEmbl flatfile qapflatall Protein,Protfeatures SpTrEmbl flatfiles, all fields indexed qapir Protein,Protfeatures Test PIR indexed by dbigcg qapirall Protein,Protfeatures Test PIR indexed by dbigcg with fields qapirexc Protein,Protfeatures Test PIR indexed by dbigcg except file pir1 qapirinc Protein,Protfeatures Test PIR indexed by dbigcg file pir1 qapxfasta Protein FASTA file swissnew entries qapxflat Protein Swissnew flatfiles qasrswww Protein,Protfeatures Remote SRS web server qaxpir Protein,Protfeatures PIR indexed by dbxgcg qaxpirall Protein,Protfeatures Test PIR indexed by dbxgcg with fields qaxpirexc Protein,Protfeatures Test PIR indexed by dbxgcg except pir1 qaxpirinc Protein,Protfeatures Test PIR indexed by dbxgcg file pir1 tpir Protein Test PIR using NBRF access for 4 files tsw Protein,Protfeatures,Text Swissprot native format with EMBL CD-ROM index tswnew Protein,Protfeatures SpTrEmbl as 3 files in native format with EMBL CD-ROM index bpembl Nucleotide,Nucfeatures BioPerl OBDA index of test EMBL bpgb Nucleotide,Nucfeatures BioPerl OBDA index of test GenBank ena Nucleotide,Nucfeatures ENA via URL qanfasta Nucleotide FASTA file EMBL rodents qanfastaall Nucleotide FASTA file EMBL rodents, all fields indexed qanflat Nucleotide,Nucfeatures,Refseq EMBL flatfiles qanflatall Nucleotide,Nucfeatures,Refseq EMBL flatfiles qanflatexc Nucleotide,Nucfeatures EMBL flatfiles, no rodent file qanflatinc Nucleotide,Nucfeatures EMBL flatfiles, only rodent file qangcg Nucleotide,Nucfeatures GCG format test EMBL qangcgall Nucleotide,Nucfeatures GCG format test EMBL qangcgexc Nucleotide,Nucfeatures GCG format test EMBL without prokaryotes qangcginc Nucleotide,Nucfeatures GCG format test EMBL only prokaryotes qanxfasta Nucleotide FASTA file EMBL rodents qanxfastaall Nucleotide FASTA file EMBL rodents, all fields indexed qanxflat Nucleotide,Nucfeatures,Refseq EMBL flatfiles qanxflatall Nucleotide,Nucfeatures,Refseq EMBL flatfiles, all fields indexed qanxflatexc Nucleotide,Nucfeatures,Refseq EMBL flatfiles, no rodent file qanxflatinc Nucleotide,Nucfeatures EMBL flatfiles, only rodent file qanxgcg Nucleotide,Nucfeatures GCG format EMBL qanxgcgall Nucleotide,Nucfeatures GCG format EMBL indexed by dbxgcg with query fields qanxgcgexc Nucleotide,Nucfeatures GCG format EMBL without prokaryotes qanxgcginc Nucleotide,Nucfeatures GCG format EMBL only prokaryotes qawfasta Nucleotide FASTA file wormpep entries qawxfasta Nucleotide FASTA file wormpep entries qaxembl Nucleotide,Nucfeatures,Refseq EMBL flatfiles tembl Nucleotide,Refseq,Nucfeatures EMBL in native format with EMBL CD-ROM index temblall Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index temblrest Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL CD-ROM index temblvrt Nucleotide,Nucfeatures EMBL in native format with EMBL CD-ROM index tensembldasgrch37 Nucleotide Homo_sapiens Reference server based on GRCh37 assembly testdb Nucleotide test sequence data tgb Nucleotide,Nucfeatures Genbank by SRS at DKFZ tgenbank Nucleotide,Nucfeatures Test GenBank in native format with EMBL CD-ROM index tgenedashuman Nucleotide The Ensembl human Gene_ID reference source tflybase Features Flybase CHADO server tgenedb Features GeneDb CHADO server ttax Taxonomy NCBI taxonomy test data taxon Taxonomy NCBI taxonomy drcat Resource Data Resource Catalogue tedam Obo Test EDAM using dbxedam test indexes tobo Obo Test EDAM using dbxobo test indexes chebi Obo Chemical Entities of Biological Interest eco Obo Evidence code ontology edam Obo EMBRACE Data and Methods ontology edam_data Obo EMBRACE Data and Methods ontology (data) edam_format Obo EMBRACE Data and Methods ontology (formats) edam_identifier Obo EMBRACE Data and Methods ontology (identifiers) edam_operation Obo EMBRACE Data and Methods ontology (operations) edam_topic Obo EMBRACE Data and Methods ontology (topics) go Obo Gene Ontology go_component Obo Gene Ontology (cellular components) go_function Obo Gene Ontology (molecular functions) go_process Obo Gene Ontology (biological processes) pw Obo Pathways ontology ro Obo Relations ontology so Obo Sequence ontology swo Obo Software ontology |
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 | Generate server cache file for DAS servers or for the DAS registry |
| cachedbfetch | Generate server cache file for Dbfetch/WSDbfetch data sources |
| cacheebeyesearch | Generate server cache file for EB-eye search domains |
| cacheensembl | Generate server cache file for an Ensembl server |
| dbtell | Display information about a public database |
| servertell | Display information about a public server |
| showserver | Display 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.