|   | textsearch | 
Search for 'lactose':
| % textsearch tsw:* 'lactose' Search sequence documentation. Slow, use SRS and Entrez! Output file [edd1_rat.textsearch]: | 
Go to the input files for this example
Go to the output files for this example
Example 2
Search for 'lactose' or 'permease' in E.coli proteins:
| % textsearch tsw:*_ecoli 'lactose | permease' Search sequence documentation. Slow, use SRS and Entrez! Output file [laci_ecoli.textsearch]: | 
Go to the output files for this example
Example 3
Output a search for 'lacz' formatted with HTML to a file:
| % textsearch tembl:* 'lacz' -html -outfile embl.lacz.html Search sequence documentation. Slow, use SRS and Entrez! | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input 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 (Any string is accepted)
  [-outfile]           outfile    [*.textsearch] Output file name
   Additional (Optional) qualifiers:
   -casesensitive      boolean    [N] Do a case-sensitive search
   -html               boolean    [N] Format output as an HTML table
   Advanced (Unprompted) qualifiers:
   -only               boolean    [N] 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            boolean    [@(!$(only))] Display column headings
   -usa                boolean    [@(!$(only))] Display the USA of the
                                  sequence
   -accession          boolean    [@(!$(only))] Display 'accession' column
   -name               boolean    [@(!$(only))] Display 'name' column
   -description        boolean    [@(!$(only))] Display 'description' column
   Associated qualifiers:
   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name
   "-outfile" associated qualifiers
   -odirectory3        string     Output directory
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) | (Gapped) sequence(s) filename and optional format, or reference (input 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 | 
| [-outfile] (Parameter 3) | Output file name | Output file | <*>.textsearch | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| -casesensitive | Do a case-sensitive search | Boolean value Yes/No | No | 
| -html | Format output as an HTML table | Boolean value Yes/No | No | 
| Advanced (Unprompted) 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' | Boolean value Yes/No | No | 
| -heading | Display column headings | Boolean value Yes/No | @(!$(only)) | 
| -usa | Display the USA of the sequence | Boolean value Yes/No | @(!$(only)) | 
| -accession | Display 'accession' column | Boolean value Yes/No | @(!$(only)) | 
| -name | Display 'name' column | Boolean value Yes/No | @(!$(only)) | 
| -description | Display 'description' column | Boolean value Yes/No | @(!$(only)) | 
| # Search for: lactose tsw-id:LACI_ECOLI LACI_ECOLI P03023 Lactose operon repressor. tsw-id:LACY_ECOLI LACY_ECOLI P02920 Lactose permease (Lactose-proton symport). | 
| # Search for: lactose | permease tsw-id:LACI_ECOLI LACI_ECOLI P03023 Lactose operon repressor. tsw-id:LACY_ECOLI LACY_ECOLI P02920 Lactose permease (Lactose-proton symport). | 
| 
 | 
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 sequence with restriction 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 | 
| sixpack | Display a DNA sequence with 6-frame translation and ORFs | 
| 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 |