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:paamir Displays some simple information about sequences # USA Name Accession Type Length %GC Description tembl-id:PAAMIR PAAMIR 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:paamir -nousa Displays some simple information about sequences # Name Accession Type Length %GC Description PAAMIR 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:paamir -only -name -length Displays some simple information about sequences PAAMIR 2167 |
Example 4
Display only the description of a sequence:
% infoseq tembl:paamir -only -desc Displays some simple information about sequences Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation |
Example 5
Display the type of a sequence:
% infoseq tembl:paamir -only -type Displays some simple information about sequences N |
Example 6
Display information formatted with HTML:
% infoseq tembl:paamir -html Displays some simple information about sequences
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Standard (Mandatory) qualifiers: [-sequence] seqall Sequence database USA Additional (Optional) qualifiers: -outfile outfile If you enter the name of a file here then this program will write the sequence details into that file. -html boolean Format output as an HTML table Advanced (Unprompted) qualifiers: -only boolean 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' -heading boolean Display column headings -usa boolean Display the USA of the sequence -name boolean Display 'name' column -accession boolean Display 'accession' column -gi boolean Display 'GI' column -version boolean Display 'version' column -type boolean Display 'type' column -length boolean Display 'length' column -pgc boolean Display 'percent GC content' column -description boolean 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 deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database 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 | |
-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 |
-heading | Display column headings | Boolean value Yes/No | @(!$(only)) |
-usa | Display the USA of the sequence | Boolean value Yes/No | @(!$(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 PAAMIR standard; DNA; PRO; 2167 BP. XX AC X13776; M43175; XX SV X13776.1 XX DT 19-APR-1989 (Rel. 19, Created) DT 17-FEB-1997 (Rel. 50, Last updated, Version 22) 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; gamma subdivision; 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 MEDLINE; 89211409. 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. 246:39-43(1989). XX RN [3] RP 1-1292 RX MEDLINE; 91317707. 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. 173:4914-4921(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 SWISS-PROT; P10932; AMIR_PSEAE. DR SWISS-PROT; P27017; AMIC_PSEAE. DR SWISS-PROT; Q51417; AMIS_PSEAE. [Part of this file has been deleted for brevity] FT phenotype" FT /replace="" FT /gene="amiC" 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 |