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EMBOSS: textsearch |
% textsearch swissprot:\* 'lacz'
Search for matches to 'lacz' or 'permease' in E.coli proteins
% textsearch swissprot:\*_ecoli 'lacZ | permease'
Output a search for 'transport' formatted with HTML to a file
% textsearch embl:\* 'transport' -html -outfile embl.transport
Mandatory qualifiers:
[-sequence] seqall Sequence database USA
[-pattern] string The search pattern is a regular expression.
Use a | to indicate OR.
For example:
human|mouse
will find text with either 'human' OR
'mouse' in the text
Optional qualifiers:
-casesensitive bool Do a case-sensitive search
-html bool Format output as an HTML table
-outfile outfile If you enter the name of a file here then
this program will write the sequence details
into that file.
Advanced qualifiers:
-only bool This is a way of shortening the command line
if you only want a few things to be
displayed. Instead of specifying:
'-nohead -noname -nousa -noacc -nodesc'
to get only the name output, you can specify
'-only -name'
-heading bool Display column headings
-usa bool Display the USA of the sequence
-accession bool Display 'accession' column
-name bool Display 'name' column
-description bool Display 'description' column
General qualifiers:
-help bool report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
|
| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
| [-pattern] (Parameter 2) |
The search pattern is a regular expression. Use a | to indicate OR. For example: human|mouse will find text with either 'human' OR 'mouse' in the text | Any string is accepted | An empty string is accepted |
| Optional qualifiers | Allowed values | Default | |
| -casesensitive | Do a case-sensitive search | Yes/No | No |
| -html | Format output as an HTML table | Yes/No | No |
| -outfile | If you enter the name of a file here then this program will write the sequence details into that file. | Output file | stdout |
| Advanced qualifiers | Allowed values | Default | |
| -only | This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -noname -nousa -noacc -nodesc' to get only the name output, you can specify '-only -name' | Yes/No | No |
| -heading | Display column headings | Yes/No | @(!$(only)) |
| -usa | Display the USA of the sequence | Yes/No | @(!$(only)) |
| -accession | Display 'accession' column | Yes/No | @(!$(only)) |
| -name | Display 'name' column | Yes/No | @(!$(only)) |
| -description | Display 'description' column | Yes/No | @(!$(only)) |
--------------------------------------------------------------------------- # Search for: TRANSPORT ANSP_SALTY L-ASPARAGINE PERMEASE (L-ASPARAGINE TRANSPORT PROTEIN). CYST_SALTY SULFATE TRANSPORT SYSTEM PERMEASE PROTEIN CYST (FRAGMENT). HISM_SALTY HISTIDINE TRANSPORT SYSTEM PERMEASE PROTEIN HISM. HISQ_SALTY HISTIDINE TRANSPORT SYSTEM PERMEASE PROTEIN HISQ. LIVH_SALTY HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT PERMEASE ... LIVM_SALTY HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT PERMEASE ... MALF_SALTY MALTOSE TRANSPORT SYSTEM PERMEASE PROTEIN MALF. MALG_SALTY MALTOSE TRANSPORT SYSTEM PERMEASE PROTEIN MALG. MELB_SALTY MELIBIOSE CARRIER PROTEIN (THIOMETHYLGALACTOSIDE PERMEASE II) ... MGLC_SALTY GALACTOSIDE TRANSPORT SYSTEM PERMEASE PROTEIN MGLC. OPPB_SALTY OLIGOPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN OPPB. OPPC_SALTY OLIGOPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN OPPC. POTB_SALTY SPERMIDINE/PUTRESCINE TRANSPORT SYSTEM PERMEASE PROTEIN POTB ... PROW_SALTY GLYCINE BETAINE/L-PROLINE TRANSPORT SYSTEM PERMEASE PROTEIN ... SAPB_SALTY PEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN SAPB. SAPC_SALTY PEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN SAPC. ---------------------------------------------------------------------------
The first column in the name or ID of each sequence. The remaining text is the description line of the sequence.
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 supplier by the user.
The lines of out information are guaranteed not to have trailing white-space at the end. So if '-nodesc' is used, there will not be any whitespace after the ID name.
| 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 a sequence with restriction cut sites, translation etc |
| seealso | Finds programs sharing group names |
| showalign | Displays a multiple sequence alignment |
| showdb | Displays information on the currently available databases |
| showfeat | Show features of a sequence |
| showseq | Display a sequence with features, translation etc |
| 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 |