📄 showdb.txt
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showdb Function Displays information on the currently available databasesDescription 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 swissnewqapblastall P OK OK OK BLAST swissnew, all fields indexedqapblastsplit P OK OK OK BLAST swissnew split in 5 filesqapblastsplitexc P OK OK OK BLAST swissnew split in 5 files, not file 02qapblastsplitinc P OK OK OK BLAST swissnew split in 5 files, only file 02qapfasta P OK OK OK FASTA file swissnew entriesqapflat P OK OK OK Swissnew flatfilesqapflatall P OK OK OK Swissnew flatfiles, all fields indexedqapflatexc P OK OK OK Swissnew flatfiles, no updated sequence fileqapflatinc P OK OK OK Swissnew flatfiles, only updated sequence fileqapir P OK OK OK PIRqapirall P OK OK OK PIRqapirinc P OK OK OK PIRqapxfasta P OK OK OK FASTA file swissnew entriesqapxflat P OK OK OK Swissnew flatfilesqapxflatexc P OK OK OK Swissnew flatfiles, no updated sequence fileqapxflatinc P OK OK OK Swissnew flatfiles, only updated sequence fileqaxpir P OK OK OK PIRqaxpirall P OK OK OK PIRqaxpirinc P OK OK OK PIRtpir P OK OK OK PIR using NBRF access for 4 filestsw P OK OK OK Swissprot native format with EMBL CD-ROM indextswnew P OK OK OK Swissnew as 3 files in native format with EMBL CD-ROM indextwp P OK OK OK EMBL new in native format with EMBL CD-ROM indexgenbanksrs N OK - - Genbank IDsqanfasta N OK OK OK FASTA file EMBL rodentsqanfastaall N OK OK OK FASTA file EMBL rodents, all fields indexedqanflat N OK OK OK EMBL flatfilesqangcg N OK OK OK GCG format EMBLqangcgall N OK OK OK GCG format EMBLqangcgexc N OK OK OK GCG format EMBL without prokaryotesqangcginc N OK OK OK GCG format EMBL only prokaryotesqanxfasta N OK OK OK FASTA file EMBL rodentsqanxfastaall N OK OK OK FASTA file EMBL rodents, all fields indexedqanxflat N OK OK OK EMBL flatfilesqanxflatall N OK OK OK EMBL flatfiles, all fields indexedqanxgcg N OK OK OK GCG format EMBLqanxgcgall N OK OK OK GCG format EMBLqanxgcgexc N OK OK OK GCG format EMBL without prokaryotesqanxgcginc N OK OK OK GCG format EMBL only prokaryotesqapirexc N OK OK OK PIRqasrswww N OK - - Remote SRS web serverqawfasta N OK OK OK FASTA file wormpep entriesqawxfasta N OK OK OK FASTA file wormpep entriesqaxpirexc N OK OK OK PIRtembl N OK OK OK EMBL in native format with EMBL CD-ROM indextemblall N - - OK EMBL in native format with EMBL CD-ROM indextemblrest N - - OK EMBL in native format with EMBL CD-ROM indextemblvrt N - - OK EMBL in native format with EMBL CD-ROM indextgb N OK - - Genbank IDstgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index Example 2 Write the results to a file:% showdb -outfile showdb.out Displays information on 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 02 qapfasta P OK OK OK FASTA file swissnew entries qapflat P OK OK OK Swissnew flatfiles qapflatall P OK OK OK Swissnew flatfiles, all fields indexed qapflatexc P OK OK OK Swissnew flatfiles, no updated sequence file qapflatinc P OK OK OK Swissnew flatfiles, only updated sequence file 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 qapxflatexc P OK OK OK Swissnew flatfiles, no updated sequence file qapxflatinc P OK OK OK Swissnew flatfiles, only updated sequence file 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 Swissnew as 3 files in native format with EMBL CD-ROMindex 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 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 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 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 swissnewqapblastall P OK OK OK BLAST swissnew, all fields indexedqapblastsplit P OK OK OK BLAST swissnew split in 5 filesqapblastsplitexc P OK OK OK BLAST swissnew split in 5 files, not file 02qapblastsplitinc P OK OK OK BLAST swissnew split in 5 files, only file 02qapfasta P OK OK OK FASTA file swissnew entriesqapflat P OK OK OK Swissnew flatfilesqapflatall P OK OK OK Swissnew flatfiles, all fields indexedqapflatexc P OK OK OK Swissnew flatfiles, no updated sequence fileqapflatinc P OK OK OK Swissnew flatfiles, only updated sequence file⌨️ 快捷键说明
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