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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 |