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|
<HTML>
<HEAD>
<TITLE>
EMBOSS: infoseq
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
infoseq
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Displays some simple information about sequences
<H2>
Description
</H2>
This is a small utility to list the sequences' USA, name, accession
number, type (nucleic or protein), length, percentage C+G, and/or
description.
<p>
Any combination of these types of information can be easily selected or
unselected.
<p>
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.
<H2>
Usage
</H2>
<b>Here is a sample session with infoseq</b>
<p>
Display information on a sequence:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>infoseq tembl:x13776 </b>
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
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><p>
<p>
<b>Example 2</b>
<p>
Don't display the USA of a sequence:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>infoseq tembl:x13776 -nousa </b>
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
</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 3</b>
<p>
Display only the name and length of a sequence:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>infoseq tembl:x13776 -only -name -length </b>
Displays some simple information about sequences
Name Length
X13776 2167
</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 4</b>
<p>
Display only the description of a sequence:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>infoseq tembl:x13776 -only -desc </b>
Displays some simple information about sequences
Description
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 5</b>
<p>
Display the type of a sequence:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>infoseq tembl:x13776 -only -type </b>
Displays some simple information about sequences
Type
N
</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 6</b>
<p>
Display information formatted with HTML:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>infoseq tembl:x13776 -html </b>
Displays some simple information about sequences
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>USA</th><th>Database</th><th>Name</th><th>Accession</th><th>Type</th><th>Length</th><th>%GC</th><th>Description</th></tr>
<tr><td>tembl-id:X13776</td><td>tembl</td><td>X13776</td><td>X13776</td><td>N</td><td>2167</td><td>66.54</td><td>Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation</td></tr>
</table>
</pre></td></tr></table><p>
<p>
<p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>(Gapped) sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-outfile</td>
<td>If you enter the name of a file here then this program will write the sequence details into that file.</td>
<td>Output file</td>
<td>stdout</td>
</tr>
<tr>
<td>-html</td>
<td>Format output as an HTML table</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-[no]columns</td>
<td>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.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-delimiter</td>
<td>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.</td>
<td>Any string is accepted</td>
<td>|</td>
</tr>
<tr>
<td>-only</td>
<td>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'</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-[no]heading</td>
<td>Display column headings</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-usa</td>
<td>Display the USA of the sequence</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>
<tr>
<td>-database</td>
<td>Display 'database' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>
<tr>
<td>-name</td>
<td>Display 'name' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>
<tr>
<td>-accession</td>
<td>Display 'accession' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>
<tr>
<td>-gi</td>
<td>Display 'GI' column</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-version</td>
<td>Display 'version' column</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-type</td>
<td>Display 'type' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>
<tr>
<td>-length</td>
<td>Display 'length' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>
<tr>
<td>-pgc</td>
<td>Display 'percent GC content' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>
<tr>
<td>-description</td>
<td>Display 'description' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>infoseq</b> reads any sequence USAs.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:x13776</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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
<font color=red> [Part of this file has been deleted for brevity]</font>
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
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
The output is displayed on the screen (stdout) by default.
<p>
<p>
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:
<ul>
<li>The USA (Uniform Sequence Address) that EMBOSS can use to read in the
sequence.
<li>The name or ID of the sequence. If this is not known then '-' is
output.
<li>The accession number. If this is not known then '-' is
output.
<li>The type ('N' is nucleic, 'P' is protein).
<li>The sequence length.
<li>The description line of the sequence. This may be blank.
</ul>
<p>
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.
<p>
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.
<p>
The lines of out information are guaranteed not to have trailing
white-space at the end.
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
This program was written to make it easier to get some specific bits
of information on a sequence for use in small perl scripts.
This Perl code fragment to get the type of a sequence is typical:
<pre>
$type = `$PATH_TO_EMBOSS/infoseq $sequence -auto -only -type`;
chomp $type;
</pre>
<p>
You may find other uses for it, of course.
<p>
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'.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0
<H2>
Known bugs
</H2>
None noted.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="infoalign.html">infoalign</a></td>
<td>Information on a multiple sequence alignment</td>
</tr>
<tr>
<td><a href="seealso.html">seealso</a></td>
<td>Finds programs sharing group names</td>
</tr>
<tr>
<td><a href="showdb.html">showdb</a></td>
<td>Displays information on the currently available databases</td>
</tr>
<tr>
<td><a href="textsearch.html">textsearch</a></td>
<td>Search sequence documentation. Slow, use SRS and Entrez!</td>
</tr>
<tr>
<td><a href="tfm.html">tfm</a></td>
<td>Displays a program's help documentation manual</td>
</tr>
<tr>
<td><a href="whichdb.html">whichdb</a></td>
<td>Search all databases for an entry</td>
</tr>
<tr>
<td><a href="wossname.html">wossname</a></td>
<td>Finds programs by keywords in their one-line documentation</td>
</tr>
</table>
<ul>
<li><a href="geecee.html">geecee</a> - Calculates the fractional GC
content of a nucleic acid sequence
</ul>
<H2>
Author(s)
</H2>
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
<H2>
History
</H2>
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>
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