|   | infoseq | 
Any combination of these types of information can be easily selected or unselected.
By default, the output file starts each line with the USA of the sequence being described, so the output file is a list file that can be manually edited and read in by any other EMBOSS program that can read in one or more sequence to be analysed.
Display information on a sequence:
| % infoseq tembl:x13776 Displays some simple information about sequences USA Database Name Accession Type Length %GC Description tembl-id:X13776 tembl X13776 X13776 N 2167 66.54 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation | 
Go to the input files for this example
Example 2
Don't display the USA of a sequence:
| % infoseq tembl:x13776 -nousa Displays some simple information about sequences Database Name Accession Type Length %GC Description tembl X13776 X13776 N 2167 66.54 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation | 
Example 3
Display only the name and length of a sequence:
| % infoseq tembl:x13776 -only -name -length Displays some simple information about sequences Name Length X13776 2167 | 
Example 4
Display only the description of a sequence:
| % infoseq tembl:x13776 -only -desc Displays some simple information about sequences Description Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation | 
Example 5
Display the type of a sequence:
| % infoseq tembl:x13776 -only -type Displays some simple information about sequences Type N | 
Example 6
Display information formatted with HTML:
| % infoseq tembl:x13776 -html Displays some simple information about sequences 
 | 
| 
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
   Additional (Optional) qualifiers:
   -outfile            outfile    [stdout] If you enter the name of a file
                                  here then this program will write the
                                  sequence details into that file.
   -html               boolean    [N] Format output as an HTML table
   Advanced (Unprompted) qualifiers:
   -[no]columns        boolean    [Y] Set this option on (Y) to print the
                                  sequence information into neat, aligned
                                  columns in the output file. Alternatively,
                                  leave it unset (N), in which case the
                                  information records will be delimited by a
                                  character, which you may specify by using
                                  the -delimiter option. In other words, if
                                  -columns is set on, the -delimiter option is
                                  overriden.
   -delimiter          string     [|] This string, which is usually a single
                                  character only, is used to delimit
                                  individual records in the text output file.
                                  It could be a space character, a tab
                                  character, a pipe character or any other
                                  character or string. (Any string is
                                  accepted)
   -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 -noacc -notype -nopgc
                                  -nodesc'
                                  to get only the length output, you can
                                  specify
                                  '-only -length'
   -[no]heading        boolean    [Y] Display column headings
   -usa                boolean    [@(!$(only))] Display the USA of the
                                  sequence
   -database           boolean    [@(!$(only))] Display 'database' column
   -name               boolean    [@(!$(only))] Display 'name' column
   -accession          boolean    [@(!$(only))] Display 'accession' column
   -gi                 boolean    [N] Display 'GI' column
   -version            boolean    [N] Display 'version' column
   -type               boolean    [@(!$(only))] Display 'type' column
   -length             boolean    [@(!$(only))] Display 'length' column
   -pgc                boolean    [@(!$(only))] Display 'percent GC content'
                                  column
   -description        boolean    [@(!$(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
   -odirectory         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 | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| -outfile | If you enter the name of a file here then this program will write the sequence details into that file. | Output file | stdout | 
| -html | Format output as an HTML table | Boolean value Yes/No | No | 
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -[no]columns | Set this option on (Y) to print the sequence information into neat, aligned columns in the output file. Alternatively, leave it unset (N), in which case the information records will be delimited by a character, which you may specify by using the -delimiter option. In other words, if -columns is set on, the -delimiter option is overriden. | Boolean value Yes/No | Yes | 
| -delimiter | This string, which is usually a single character only, is used to delimit individual records in the text output file. It could be a space character, a tab character, a pipe character or any other character or string. | Any string is accepted | | | 
| -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 -noacc -notype -nopgc -nodesc' to get only the length output, you can specify '-only -length' | Boolean value Yes/No | No | 
| -[no]heading | Display column headings | Boolean value Yes/No | Yes | 
| -usa | Display the USA of the sequence | Boolean value Yes/No | @(!$(only)) | 
| -database | Display 'database' column | Boolean value Yes/No | @(!$(only)) | 
| -name | Display 'name' column | Boolean value Yes/No | @(!$(only)) | 
| -accession | Display 'accession' column | Boolean value Yes/No | @(!$(only)) | 
| -gi | Display 'GI' column | Boolean value Yes/No | No | 
| -version | Display 'version' column | Boolean value Yes/No | No | 
| -type | Display 'type' column | Boolean value Yes/No | @(!$(only)) | 
| -length | Display 'length' column | Boolean value Yes/No | @(!$(only)) | 
| -pgc | Display 'percent GC content' column | Boolean value Yes/No | @(!$(only)) | 
| -description | Display 'description' column | Boolean value Yes/No | @(!$(only)) | 
| 
ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
XX
DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW   aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS   Pseudomonas aeruginosa
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
XX
RN   [1]
RP   1167-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
RN   [2]
RP   1167-2167
RX   DOI; 10.1016/0014-5793(89)80249-2.
RX   PUBMED; 2495988.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
RT   aeruginosa";
RL   FEBS Lett. 246(1-2):39-43(1989).
XX
RN   [3]
RP   1-1292
RX   PUBMED; 1907262.
RA   Wilson S., Drew R.;
RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT   product.";
RL   J. Bacteriol. 173(16):4914-4921(1991).
XX
RN   [4]
RP   1-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR   GOA; Q51417.
DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
XX
  [Part of this file has been deleted for brevity]
FT                   /replace=""
FT                   /note="ClaI fragment deleted in pSW36,  constitutive
FT                   phenotype"
FT   misc_feature    1
FT                   /note="last base of an XhoI site"
FT   misc_feature    648..653
FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 causes
FT                   constitutive expression of amiE"
FT   conflict        1281
FT                   /replace="g"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
     cctcgag                                                                2167
//
 | 
The first non-blank line is the heading. This is followed by one line per sequence containing the following columns of data separated by one of more space or TAB characters:
If qualifiers to inhibit various columns of information are used, then the remaining columns of information are output in the same order as shown above, so if '-nolength' is used, the order of output is: usa, name, accession, type, description.
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> and <BODY> 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.
$type = `$PATH_TO_EMBOSS/infoseq $sequence -auto -only -type`; chomp $type;
You may find other uses for it, of course.
By default, the output file starts each line with the USA of the sequence being described, so the output file is a list file that can be manually edited and read in by other EMBOSS programs using the list-file specification of '@filename'.
| Program name | Description | 
|---|---|
| infoalign | Information on a multiple sequence alignment | 
| seealso | Finds programs sharing group names | 
| showdb | Displays information on the currently available databases | 
| textsearch | Search sequence documentation. Slow, use SRS and Entrez! | 
| 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 |