infoseq

 

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Function

Display basic information about sequences

Description

infoseq displays on screen basic information about one or more input sequences. This includes the Uniform Sequence Address (USA), name, accession number, type (nucleic or protein), length, percentage C+G and description. Any combination of these records is easily selected or unselected for display. The same information may be written to an output file which (optionally) may be formatted in an HTML table.

Usage

Here is a sample session with infoseq

Display information on a sequence:


% infoseq tembl:x13776 
Display basic 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 
Display basic 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 
Display basic information about sequences

Name           Length 
X13776         2167   

Example 4

Display only the description of a sequence:


% infoseq tembl:x13776 -only -desc 
Display basic 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 
Display basic information about sequences

Type 
N    

Example 6

Display information formatted with HTML:


% infoseq tembl:x13776 -html 
Display basic information about sequences

USADatabaseNameAccessionTypeLength%GCDescription
tembl-id:X13776temblX13776X13776N216766.54Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation

Command line arguments

   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 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. 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))

Input file format

infoseq reads any sequence USAs.

Input files for usage example

'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:x13776

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 (amiR) of
RT   Pseudomonas 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 sequence 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   InterPro; IPR003211; AmiSUreI_transpt.
DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.


  [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
//

Output file format

The output is displayed on the screen (stdout) by default.

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.

Data files

None.

Notes

There are many qualifiers to control exactly what information on the sequence is output and how it is formatted. If you only want a few fields in the output file, the command line may be shortended by preceding the appropriate qualifier with -only. For example, instead of specifying -nohead -noname -noacc -notype -nopgc -nodesc to get only the length output, you can specify -only -length.

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.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0

Known bugs

None noted.

See also

Program name Description
infoalign Display basic information about a multiple sequence alignment
infobase Return information on a given nucleotide base
inforesidue Return information on a given amino acid residue
seealso Finds programs with similar function to a specified program
showdb Displays information on configured databases
textsearch Search the textual description of sequence(s)
tfm Displays full documentation for an application
whichdb Search all sequence databases for an entry and retrieve it
wossname Finds programs by keywords in their short description

Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None