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wossname |
The program has been written on the assumption that most people will use it to quickly find the name of a program based on that program's description, so the output goes to the screen by default.
This program may find some use in automatically generating lists of EMBOSS programs and their groups for Web pages.
Search for programs with 'restrict' in their description:
% wossname restrict Finds programs by keywords in their one-line documentation SEARCH FOR 'RESTRICT' recoder Remove restriction sites but maintain the same translation remap Display a sequence with restriction cut sites, translation etc restover Finds restriction enzymes that produce a specific overhang restrict Finds restriction enzyme cleavage sites silent Silent mutation restriction enzyme scan |
Example 2
Display a listing of programs in their groups:
% wossname -search '' Finds programs by keywords in their one-line documentation ALIGNMENT CONSENSUS cons Creates a consensus from multiple alignments megamerger Merge two large overlapping nucleic acid sequences merger Merge two overlapping nucleic acid sequences ALIGNMENT DIFFERENCES diffseq Find differences between nearly identical sequences ALIGNMENT DOT PLOTS dotmatcher Displays a thresholded dotplot of two sequences dotpath Displays a non-overlapping wordmatch dotplot of two sequences dottup Displays a wordmatch dotplot of two sequences polydot Displays all-against-all dotplots of a set of sequences ALIGNMENT GLOBAL est2genome Align EST and genomic DNA sequences needle Needleman-Wunsch global alignment stretcher Finds the best global alignment between two sequences ALIGNMENT LOCAL matcher Finds the best local alignments between two sequences seqmatchall Does an all-against-all comparison of a set of sequences supermatcher Finds a match of a large sequence against one or more sequences water Smith-Waterman local alignment wordmatch Finds all exact matches of a given size between 2 sequences ALIGNMENT MULTIPLE emma Multiple alignment program - interface to ClustalW program infoalign Information on a multiple sequence alignment plotcon Plots the quality of conservation of a sequence alignment prettyplot Displays aligned sequences, with colouring and boxing showalign Displays a multiple sequence alignment tranalign Align nucleic coding regions given the aligned proteins DISPLAY abiview Reads ABI file and display the trace cirdna Draws circular maps of DNA constructs 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 a sequence with restriction cut 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 textsearch Search sequence documentation text. SRS and Entrez are faster! EDIT biosed Replace or delete sequence sections cutseq Removes a specified section from a sequence degapseq Removes gap characters from sequences descseq Alter the name or description of a sequence entret Reads and writes (returns) flatfile entries extractfeat Extract features from a sequence extractseq Extract regions from a sequence listor Writes a list file of the logical OR of two sets of sequences maskfeat Mask off features of a sequence maskseq Mask off regions of a sequence newseq Type in a short new sequence noreturn Removes carriage return from ASCII files notseq Excludes a set of sequences and writes out the remaining ones nthseq Writes one sequence from a multiple set of sequences pasteseq Insert one sequence into another revseq Reverse and complement a sequence seqret Reads and writes (returns) sequences seqretsplit Reads and writes (returns) sequences in individual files skipseq Reads and writes (returns) sequences, skipping the first few splitter Split a sequence into (overlapping) smaller sequences trimest Trim poly-A tails off EST sequences trimseq Trim ambiguous bits off the ends of sequences union Reads sequence fragments and builds one sequence vectorstrip Strips out DNA between a pair of vector sequences yank Reads a sequence range, appends the full USA to a list file ENZYME KINETICS findkm Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot FEATURE TABLES coderet Extract CDS, mRNA and translations from feature tables extractfeat Extract features from a sequence maskfeat Mask off features of a sequence showfeat Show features of a sequence twofeat Finds neighbouring pairs of features in sequences INFORMATION infoalign Information on a multiple sequence alignment infoseq Displays some simple information about sequences seealso Finds programs sharing group names showdb Displays information on the currently available databases textsearch Search sequence documentation text. SRS and Entrez are faster! 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 NUCLEIC 2D STRUCTURE einverted Finds DNA inverted repeats NUCLEIC CODON USAGE cai CAI codon adaptation index chips Codon usage statistics codcmp Codon usage table comparison cusp Create a codon usage table syco Synonymous codon usage Gribskov statistic plot NUCLEIC COMPOSITION banana Bending and curvature plot in B-DNA btwisted Calculates the twisting in a B-DNA sequence chaos Create a chaos game representation plot for a sequence compseq Counts the composition of dimer/trimer/etc words in a sequence dan Calculates DNA RNA/DNA melting temperature freak Residue/base frequency table or plot isochore Plots isochores in large DNA sequences sirna Finds siRNA duplexes in mRNA wordcount Counts words of a specified size in a DNA sequence NUCLEIC CPG ISLANDS cpgplot Plot CpG rich areas cpgreport Reports all CpG rich regions geecee Calculates the fractional GC content of nucleic acid sequences newcpgreport Report CpG rich areas newcpgseek Reports CpG rich regions NUCLEIC GENE FINDING getorf Finds and extracts open reading frames (ORFs) marscan Finds MAR/SAR sites in nucleic sequences plotorf Plot potential open reading frames showorf Pretty output of DNA translations sixpack Display a DNA sequence with 6-frame translation and ORFs syco Synonymous codon usage Gribskov statistic plot tcode Fickett TESTCODE statistic to identify protein-coding DNA wobble Wobble base plot NUCLEIC MOTIFS dreg regular expression search of a nucleotide sequence fuzznuc Nucleic acid pattern search fuzztran Protein pattern search after translation marscan Finds MAR/SAR sites in nucleic sequences NUCLEIC MUTATION msbar Mutate sequence beyond all recognition shuffleseq Shuffles a set of sequences maintaining composition NUCLEIC PRIMERS eprimer3 Picks PCR primers and hybridization oligos primersearch Searches DNA sequences for matches with primer pairs stssearch Searches a DNA database for matches with a set of STS primers NUCLEIC PROFILES profit Scan a sequence or database with a matrix or profile prophecy Creates matrices/profiles from multiple alignments prophet Gapped alignment for profiles NUCLEIC REPEATS einverted Finds DNA inverted repeats equicktandem Finds tandem repeats etandem Looks for tandem repeats in a nucleotide sequence palindrome Looks for inverted repeats in a nucleotide sequence NUCLEIC RESTRICTION recite Find changes to an enzyme site that introduce new enzyme sites recoder Remove restriction sites but maintain the same translation redata Search REBASE for enzyme name, references, suppliers etc remap Display a sequence with restriction cut sites, translation etc restover Finds restriction enzymes that produce a specific overhang restrict Finds restriction enzyme cleavage sites showseq Display a sequence with features, translation etc silent Silent mutation restriction enzyme scan NUCLEIC TRANSCRIPTION tfscan Scans DNA sequences for transcription factors NUCLEIC TRANSLATION backtranseq Back translate a protein sequence coderet Extract CDS, mRNA and translations from feature tables plotorf Plot potential open reading frames prettyseq Output sequence with translated ranges remap Display a sequence with restriction cut sites, translation etc showorf Pretty output of DNA translations showseq Display a sequence with features, translation etc sixpack Display a DNA sequence with 6-frame translation and ORFs transeq Translate nucleic acid sequences PHYLOGENY DISTANCE MATRIX distmat Creates a distance matrix from multiple alignments PROTEIN 2D STRUCTURE garnier Predicts protein secondary structure helixturnhelix Report nucleic acid binding motifs hmoment Hydrophobic moment calculation pepcoil Predicts coiled coil regions pepnet Displays proteins as a helical net pepwheel Shows protein sequences as helices tmap Displays membrane spanning regions PROTEIN 3D STRUCTURE contactcount counts specific versus non-specific contacts in a directory of cleaned protein chain contact files psiphi calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file PROTEIN COMPOSITION backtranseq Back translate a protein sequence charge Protein charge plot checktrans Reports STOP codons and ORF statistics of a protein compseq Counts the composition of dimer/trimer/etc words in a sequence emowse Protein identification by mass spectrometry freak Residue/base frequency table or plot iep Calculates the isoelectric point of a protein mwcontam Shows molwts that match across a set of files mwfilter Filter noisy molwts from mass spec output octanol Displays protein hydropathy pepinfo Plots simple amino acid properties in parallel pepstats Protein statistics pepwindow Displays protein hydropathy pepwindowall Displays protein hydropathy of a set of sequences PROTEIN MOTIFS antigenic Finds antigenic sites in proteins digest Protein proteolytic enzyme or reagent cleavage digest epestfind Finds PEST motifs as potential proteolytic cleavage sites fuzzpro Protein pattern search fuzztran Protein pattern search after translation helixturnhelix Report nucleic acid binding motifs oddcomp Finds protein sequence regions with a biased composition patmatdb Search a protein sequence with a motif patmatmotifs Search a PROSITE motif database with a protein sequence pepcoil Predicts coiled coil regions preg Regular expression search of a protein sequence pscan Scans proteins using PRINTS sigcleave Reports protein signal cleavage sites PROTEIN MUTATION msbar Mutate sequence beyond all recognition shuffleseq Shuffles a set of sequences maintaining composition PROTEIN PROFILES profit Scan a sequence or database with a matrix or profile prophecy Creates matrices/profiles from multiple alignments prophet Gapped alignment for profiles PROTEIN SEQUENCE ALIGNMENT contactalign EMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm UTILS DATABASE CREATION aaindexextract Extract data from AAINDEX cutgextract Extract data from CUTG printsextract Extract data from PRINTS prosextract Builds the PROSITE motif database for patmatmotifs to search rebaseextract Extract data from REBASE tfextract Extract data from TRANSFAC UTILS DATABASE INDEXING dbiblast Index a BLAST database dbifasta Index a fasta database dbiflat Index a flat file database dbigcg Index a GCG formatted database UTILS MISC embossdata Finds or fetches the data files read in by the EMBOSS programs embossversion Writes the current EMBOSS version number |
Example 3
Display an alphabetic listing of all programs:
% wossname -search '' -alphabetic Finds programs by keywords in their one-line documentation ALPHABETIC LIST OF PROGRAMS aaindexextract Extract data from AAINDEX abiview Reads ABI file and display the trace antigenic Finds antigenic sites in proteins backtranseq Back translate a protein sequence banana Bending and curvature plot in B-DNA biosed Replace or delete sequence sections btwisted Calculates the twisting in a B-DNA sequence cai CAI codon adaptation index chaos Create a chaos game representation plot for a sequence charge Protein charge plot checktrans Reports STOP codons and ORF statistics of a protein chips Codon usage statistics cirdna Draws circular maps of DNA constructs codcmp Codon usage table comparison coderet Extract CDS, mRNA and translations from feature tables compseq Counts the composition of dimer/trimer/etc words in a sequence cons Creates a consensus from multiple alignments contactalign EMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm contactcount counts specific versus non-specific contacts in a directory of cleaned protein chain contact files cpgplot Plot CpG rich areas cpgreport Reports all CpG rich regions cusp Create a codon usage table cutgextract Extract data from CUTG cutseq Removes a specified section from a sequence dan Calculates DNA RNA/DNA melting temperature dbiblast Index a BLAST database dbifasta Index a fasta database dbiflat Index a flat file database dbigcg Index a GCG formatted database degapseq Removes gap characters from sequences descseq Alter the name or description of a sequence diffseq Find differences between nearly identical sequences digest Protein proteolytic enzyme or reagent cleavage digest distmat Creates a distance matrix from multiple alignments dotmatcher Displays a thresholded dotplot of two sequences dotpath Displays a non-overlapping wordmatch dotplot of two sequences dottup Displays a wordmatch dotplot of two sequences dreg regular expression search of a nucleotide sequence einverted Finds DNA inverted repeats embossdata Finds or fetches the data files read in by the EMBOSS programs embossversion Writes the current EMBOSS version number emma Multiple alignment program - interface to ClustalW program emowse Protein identification by mass spectrometry entret Reads and writes (returns) flatfile entries epestfind Finds PEST motifs as potential proteolytic cleavage sites eprimer3 Picks PCR primers and hybridization oligos equicktandem Finds tandem repeats est2genome Align EST and genomic DNA sequences etandem Looks for tandem repeats in a nucleotide sequence extractfeat Extract features from a sequence extractseq Extract regions from a sequence findkm Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot freak Residue/base frequency table or plot fuzznuc Nucleic acid pattern search fuzzpro Protein pattern search fuzztran Protein pattern search after translation garnier Predicts protein secondary structure geecee Calculates the fractional GC content of nucleic acid sequences getorf Finds and extracts open reading frames (ORFs) helixturnhelix Report nucleic acid binding motifs hmoment Hydrophobic moment calculation iep Calculates the isoelectric point of a protein infoalign Information on a multiple sequence alignment infoseq Displays some simple information about sequences isochore Plots isochores in large DNA sequences lindna Draws linear maps of DNA constructs listor Writes a list file of the logical OR of two sets of sequences marscan Finds MAR/SAR sites in nucleic sequences maskfeat Mask off features of a sequence maskseq Mask off regions of a sequence matcher Finds the best local alignments between two sequences megamerger Merge two large overlapping nucleic acid sequences merger Merge two overlapping nucleic acid sequences msbar Mutate sequence beyond all recognition mwcontam Shows molwts that match across a set of files mwfilter Filter noisy molwts from mass spec output needle Needleman-Wunsch global alignment needle Protein global alignment against DNA newcpgreport Report CpG rich areas newcpgseek Reports CpG rich regions newseq Type in a short new sequence noreturn Removes carriage return from ASCII files notseq Excludes a set of sequences and writes out the remaining ones nthseq Writes one sequence from a multiple set of sequences octanol Displays protein hydropathy oddcomp Finds protein sequence regions with a biased composition palindrome Looks for inverted repeats in a nucleotide sequence pasteseq Insert one sequence into another patmatdb Search a protein sequence with a motif patmatmotifs Search a PROSITE motif database with a protein sequence pepcoil Predicts coiled coil regions pepinfo Plots simple amino acid properties in parallel pepnet Displays proteins as a helical net pepstats Protein statistics pepwheel Shows protein sequences as helices pepwindow Displays protein hydropathy pepwindowall Displays protein hydropathy of a set of sequences plotcon Plots the quality of conservation of a sequence alignment plotorf Plot potential open reading frames polydot Displays all-against-all dotplots of a set of sequences preg Regular expression search of a protein sequence prettyplot Displays aligned sequences, with colouring and boxing prettyseq Output sequence with translated ranges primersearch Searches DNA sequences for matches with primer pairs printsextract Extract data from PRINTS profit Scan a sequence or database with a matrix or profile prophecy Creates matrices/profiles from multiple alignments prophet Gapped alignment for profiles prosextract Builds the PROSITE motif database for patmatmotifs to search pscan Scans proteins using PRINTS psiphi calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file rebaseextract Extract data from REBASE recite Find changes to an enzyme site that introduce new enzyme sites recoder Remove restriction sites but maintain the same translation redata Search REBASE for enzyme name, references, suppliers etc remap Display a sequence with restriction cut sites, translation etc restover Finds restriction enzymes that produce a specific overhang restrict Finds restriction enzyme cleavage sites revseq Reverse and complement a sequence seealso Finds programs sharing group names seqmatchall Does an all-against-all comparison of a set of sequences seqret Reads and writes (returns) sequences seqretsplit Reads and writes (returns) sequences in individual files showalign Displays a multiple sequence alignment showdb Displays information on the currently available databases showfeat Show features of a sequence showorf Pretty output of DNA translations showseq Display a sequence with features, translation etc shuffleseq Shuffles a set of sequences maintaining composition sigcleave Reports protein signal cleavage sites silent Silent mutation restriction enzyme scan sirna Finds siRNA duplexes in mRNA sixpack Display a DNA sequence with 6-frame translation and ORFs skipseq Reads and writes (returns) sequences, skipping the first few splitter Split a sequence into (overlapping) smaller sequences stretcher Finds the best global alignment between two sequences stssearch Searches a DNA database for matches with a set of STS primers supermatcher Finds a match of a large sequence against one or more sequences syco Synonymous codon usage Gribskov statistic plot tcode Fickett TESTCODE statistic to identify protein-coding DNA textsearch Search sequence documentation text. SRS and Entrez are faster! tfextract Extract data from TRANSFAC tfm Displays a program's help documentation manual tfscan Scans DNA sequences for transcription factors tmap Displays membrane spanning regions tranalign Align nucleic coding regions given the aligned proteins transeq Translate nucleic acid sequences trimest Trim poly-A tails off EST sequences trimseq Trim ambiguous bits off the ends of sequences twofeat Finds neighbouring pairs of features in sequences union Reads sequence fragments and builds one sequence vectorstrip Strips out DNA between a pair of vector sequences water Smith-Waterman local alignment whichdb Search all databases for an entry wobble Wobble base plot wordcount Counts words of a specified size in a DNA sequence wordmatch Finds all exact matches of a given size between 2 sequences wossname Finds programs by keywords in their one-line documentation yank Reads a sequence range, appends the full USA to a list file |
Example 4
Display only the groups that the programs can belong to:
% wossname -search '' -groups Finds programs by keywords in their one-line documentation ALIGNMENT CONSENSUS ALIGNMENT DIFFERENCES ALIGNMENT DOT PLOTS ALIGNMENT GLOBAL ALIGNMENT LOCAL ALIGNMENT MULTIPLE DISPLAY EDIT ENZYME KINETICS FEATURE TABLES INFORMATION NUCLEIC 2D STRUCTURE NUCLEIC CODON USAGE NUCLEIC COMPOSITION NUCLEIC CPG ISLANDS NUCLEIC GENE FINDING NUCLEIC MOTIFS NUCLEIC MUTATION NUCLEIC PRIMERS NUCLEIC PROFILES NUCLEIC REPEATS NUCLEIC RESTRICTION NUCLEIC TRANSCRIPTION NUCLEIC TRANSLATION PHYLOGENY DISTANCE MATRIX PROTEIN 2D STRUCTURE PROTEIN 3D STRUCTURE PROTEIN COMPOSITION PROTEIN MOTIFS PROTEIN MUTATION PROTEIN PROFILES PROTEIN SEQUENCE ALIGNMENT UTILS DATABASE CREATION UTILS DATABASE INDEXING UTILS MISC |
Example 5
Output html tags around the list of program groups:
% wossname -groups -html -prelink '#' Finds programs by keywords in their one-line documentation Keyword to search for, or blank to list all programs:
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Example 6
Output html tags around the list of programs:
% wossname '' -html -prelink 'Apps/' -postlink '.html' -out wossname.html Finds programs by keywords in their one-line documentation |
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-search] string Enter a word or words here and a
case-independent search for it will be made
in the one-line documentation of all of the
EMBOSS programs. If no keyword is specified,
all programs will be listed.
Additional (Optional) qualifiers (* if not always prompted):
-explode boolean The groups that EMBOSS applications belong
to have two forms, exploded and not
exploded. The exploded group names are more
numerous and often vaguely phrased than the
non-exploded ones. The exploded names are
formed from definitions of the group names
that start like NAME1:NAME2 and which are
then expanded into many combinations of the
names as: 'NAME1', 'NAME2', 'NAME1 NAME2',
NAME2 NAME1'. The non-expanded names are
simply like: 'NAME1 NAME2'.
-outfile outfile Output file name
-html toggle If you are sending the output to a file,
this will format it for displaying as a
table in a WWW document.
* -prelink string If you are outputting to a file in HTML
format, you can make the program names into
hyper-links by setting this to be the first
half of the URL.
For example, if you wish the program name to
be a hyperlink to the URL:
Apps/programname.html
then if you enter
Apps/
here, then the first half of the URL before
the programname will be set.
* -postlink string If you are outputting to a file in HTML
format, you can make the program names into
hyper-links by setting this to be the second
half of the URL.
For example, if you wish the program name to
be a hyperlink to the URL:
Apps/programname.html
then if you enter '.html' here, the second
half of the URL after the programname will
be set.
-groups boolean If you use this option, then only the group
names will output to the file
-alphabetic boolean If you use this option, then you will get a
single list of the program names and
descriptions instead of the programs being
listed in their functional groups.
Advanced (Unprompted) qualifiers:
-[no]emboss boolean If you use this option then EMBOSS program
documentation will be searched. If this
option is set to be false, then only the
EMBASSY programs will be searched (if the
-embassy option is true). EMBASSY programs
are not strictly part of EMBOSS, but use the
same code libraries and share the same look
and feel, but are generally developed by
people who wish the programs to be outside
of the GNU Public Licence sheme, ie. they
may wish to charge money for them.
-[no]embassy boolean If you use this option then EMBASSY program
documentation will be searched. If this
option is set to be false, then only the
EMBOSS programs will be searched (if the
-emboss option is true). EMBASSY programs
are not strictly part of EMBOSS, but use the
same code libraries and share the same look
and feel, but are generally developed by
people who wish the programs to be outside
of the GNU Public Licence sheme, ie. they
may wish to charge money for them.
-colon boolean The groups that EMBOSS applications belong
to up to two levels, for example the primary
group 'ALIGNMENT' has several sub-groups,
or second-level groups, e.g.: CONSENSUS,
DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL,
MULTIPLE. To aid programs that parse the
output of wossname that require the names of
these subgroups, a colon ':' will be placed
between the first and second level of the
group name if this option is true. Note:
This does not apply if the group names have
been exploded with the 'explode' option.
-gui boolean This option is intended to help those who
are designing Graphical User Interfaces to
the EMBOSS applications. Some EMBOSS
programs are inappropriate for running in a
GUI, these include other menu programs and
interactive editors. This option allows you
to only report those programs that can be
run from a GUI
Associated qualifiers:
"-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 | |
|---|---|---|---|
| [-search] (Parameter 1) |
Enter a word or words here and a case-independent search for it will be made in the one-line documentation of all of the EMBOSS programs. If no keyword is specified, all programs will be listed. | Any string is accepted | An empty string is accepted |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -explode | The groups that EMBOSS applications belong to have two forms, exploded and not exploded. The exploded group names are more numerous and often vaguely phrased than the non-exploded ones. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: 'NAME1', 'NAME2', 'NAME1 NAME2', NAME2 NAME1'. The non-expanded names are simply like: 'NAME1 NAME2'. | Boolean value Yes/No | No |
| -outfile | Output file name | Output file | stdout |
| -html | If you are sending the output to a file, this will format it for displaying as a table in a WWW document. | Toggle value Yes/No | N |
| -prelink | If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the first half of the URL. For example, if you wish the program name to be a hyperlink to the URL: Apps/programname.html then if you enter Apps/ here, then the first half of the URL before the programname will be set. | Any string is accepted | An empty string is accepted |
| -postlink | If you are outputting to a file in HTML format, you can make the program names into hyper-links by setting this to be the second half of the URL. For example, if you wish the program name to be a hyperlink to the URL: Apps/programname.html then if you enter '.html' here, the second half of the URL after the programname will be set. | Any string is accepted | An empty string is accepted |
| -groups | If you use this option, then only the group names will output to the file | Boolean value Yes/No | No |
| -alphabetic | If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups. | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -[no]emboss | If you use this option then EMBOSS program documentation will be searched. If this option is set to be false, then only the EMBASSY programs will be searched (if the -embassy option is true). EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence sheme, ie. they may wish to charge money for them. | Boolean value Yes/No | Yes |
| -[no]embassy | If you use this option then EMBASSY program documentation will be searched. If this option is set to be false, then only the EMBOSS programs will be searched (if the -emboss option is true). EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence sheme, ie. they may wish to charge money for them. | Boolean value Yes/No | Yes |
| -colon | The groups that EMBOSS applications belong to up to two levels, for example the primary group 'ALIGNMENT' has several sub-groups, or second-level groups, e.g.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE. To aid programs that parse the output of wossname that require the names of these subgroups, a colon ':' will be placed between the first and second level of the group name if this option is true. Note: This does not apply if the group names have been exploded with the 'explode' option. | Boolean value Yes/No | No |
| -gui | This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors. This option allows you to only report those programs that can be run from a GUI | Boolean value Yes/No | No |
wossname reads the brief descriptions and the program groups from the ACD files. (ACD files control the parameters that the programs expect - don't worry about them unless you are writing EMBOSS programs).
The format of ACD files is documented elsewhere.
ALIGNMENT CONSENSUS
ALIGNMENT DIFFERENCES
ALIGNMENT DOT PLOTS
ALIGNMENT GLOBAL
ALIGNMENT LOCAL
ALIGNMENT MULTIPLE
DISPLAY
PROTEIN MUTATION
PROTEIN PROFILES
PROTEIN SEQUENCE ALIGNMENT
UTILS DATABASE CREATION
UTILS DATABASE INDEXING
UTILS MISC
|
If the -html, -prelink and -postlink qualifiers are 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 list of programs is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user.
A program can belong to more than one group.
The name of this program comes from its use as a favorite word of the author Terry Pratchett. It is used especially by the characters of the parrot in Eric and the dog Gaspode in Moving Pictures and Men at Arms.
| Program name | Description |
|---|---|
| infoalign | Information on a multiple sequence alignment |
| infoseq | Displays some simple information about sequences |
| seealso | Finds programs sharing group names |
| showdb | Displays information on the currently available databases |
| textsearch | Search sequence documentation text. SRS and Entrez are faster! |
| tfm | Displays a program's help documentation manual |
| whichdb | Search all databases for an entry |