|   | drfindformat | 
Please help by correcting and extending the Wiki pages.
The -sensitive qualifier also searches the definition strings.
The set of EDAM terms are then compared to entries in the Data Resource Catalogue, searching the 'efmt' EDAM format index.
| % drfindformat fasta Find public databases by format Data resource output file [drfindformat.drcat]: | 
Go to the output files for this example
| 
Find public databases by format
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-query]             string     List of EDAM data keywords (Any string)
  [-outfile]           outresource [*.drfindformat] Output data resource file
                                  name
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -sensitive          boolean    [N] By default, the query keywords are
                                  matched against the EDAM term names (and
                                  synonyms) only. This option also matches the
                                  keywords against the EDAM term definitions
                                  and will therefore (typically) report more
                                  matches.
   -[no]subclasses     boolean    [Y] Extend the query matches to include all
                                  terms which are specialisations (EDAM
                                  sub-classes) of the matched type.
   Associated qualifiers:
   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     Data resource output format
   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 | ||||
| [-query] (Parameter 1) | string | List of EDAM data keywords | Any string | |
| [-outfile] (Parameter 2) | outresource | Output data resource file name | Data resource entry | <*>.drfindformat | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -sensitive | boolean | By default, the query keywords are matched against the EDAM term names (and synonyms) only. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches. | Boolean value Yes/No | No | 
| -[no]subclasses | boolean | Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type. | Boolean value Yes/No | Yes | 
| Associated qualifiers | ||||
| "-outfile" associated outresource qualifiers | ||||
| -odirectory2 -odirectory_outfile | string | Output directory | Any string | |
| -oformat2 -oformat_outfile | string | Data resource output format | 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 | 
The output is a standard EMBOSS resource file.
The results can be output in one of several styles by using the command-line qualifier -oformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: drcat, basic, wsbasic, list.
See: http://emboss.sf.net/docs/themes/ResourceFormats.html for further information on resource formats.
| 
ID      UniProtKB_Swiss-Prot
IDalt   SwissProt
Name    Universal protein resource knowledge base / Swiss-Prot
Desc    Section of the UniProt knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature
URL     http://www.uniprot.org
Taxon   1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid  3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    EMBL_explicit | UniProt accession
Query    Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query    Sequence record full | Text | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query    Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml
Query    Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf
Query    Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession | P12345
ID      UniProtKB_TrEMBL
IDalt   TrEMBL
Name    Universal protein resource knowledge base / Swiss-Prot
Desc    Section of the UniProt knowledgebase, containing computationally analysed records waiting for full manual annotation
URL     http://www.uniprot.org/
Taxon   1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid  3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_FT | None
Query    Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query    Sequence record full | Text | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query    Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml
Query    Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf
Query    Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession | Q00177
ID      Ensembl
Acc     DB-0023
Name    Ensembl eukaryotic genome annotation project
Desc    Genome databases for vertebrates and other eukaryotic species.
URL     http://www.ensembl.org/
Cat     Genome annotation databases
Taxon   33208 | Metazoa
EDAMtpc 2818 | Eukaryotes
  [Part of this file has been deleted for brevity]
Query    Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query    Sequence record full | uniprot | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query    Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml
Query    Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf
Query    Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession | P12345
ID      dbEST
Name    dbEST database of EST sequences
Desc    dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
URL     http://www.ncbi.nlm.nih.gov/dbEST/
Cat     Not available
Taxon   1 | all
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMdat 0849 | Sequence record
EDAMid  2314 | GI number
EDAMid  1105 | dbEST accession
EDAMfmt 2310 | FASTA-HTML
EDAMfmt 2532 | GenBank-HTML
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query    Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query    Sequence record | HTML {est} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query    Sequence record | HTML {docsum} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query    Sequence record | FASTA-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query    Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query    Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query    Sequence record | HTML {est} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query    Sequence record | HTML {docsum} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query    Sequence record | FASTA-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query    Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Example dbEST accession | f12345
Example GI number | 706694
ID      REDIdb
Name    RNA editing database (REDIdb)
Desc    Sequences post-transcriptionally modified by RNA editing from primary databases and literature. All editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored.
URL     http://biologia.unical.it/py_script/overview.html
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMdat 2043 | Sequence record lite
EDAMdat 1383 | Sequence alignment (nucleic acid)
EDAMid  2781 | REDIdb ID
EDAMfmt 2310 | FASTA-HTML
EDAMfmt 2331 | HTML
Query    Sequence record lite {REDIdb entry} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/retrieve.py?query=%s
Query    Sequence record lite {REDIdb fasta} | FASTA-HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/fasta.py?query=%s
Query    Sequence alignment (nucleic acid) {REDIdb overview} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/display.py?query=%s
Query    Sequence alignment (nucleic acid) {REDIdb alignment} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/align.py?query=%s
Example REDIdb ID  | EDI_000000002
 | 
| Program name | Description | 
|---|---|
| drfinddata | Find public databases by data type | 
| drfindid | Find public databases by identifier | 
| drfindresource | Find public databases by resource | 
| drget | Get data resource entries | 
| drtext | Get data resource entries complete text | 
| edamdef | Find EDAM ontology terms by definition | 
| edamhasinput | Find EDAM ontology terms by has_input relation | 
| edamhasoutput | Find EDAM ontology terms by has_output relation | 
| edamisformat | Find EDAM ontology terms by is_format_of relation | 
| edamisid | Find EDAM ontology terms by is_identifier_of relation | 
| edamname | Find EDAM ontology terms by name | 
| wossdata | Find programs by EDAM data | 
| wossinput | Find programs by EDAM input data | 
| wossoperation | Find programs by EDAM operation | 
| wossoutput | Find programs by EDAM output data | 
| wossparam | Find programs by EDAM parameter | 
| wosstopic | Find programs by EDAM topic | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.