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EMBOSS: seealso |
It does this by noting the functional groups that the program belongs to and reporting any programs which share those functional groups.
The functional groups of a program are set in the ACD file (this is the part of the program in the EMBOSS system which specifies the required parameters, some help on the parameters, the one-line description of the program, etc.) Normally the names of the groups are fairly specific, such as: "NUCLEIC COMPOSITION", resulting in the reporting of only a tightly restricted set of other programs also dealing with the analysis of "NUCLEIC COMPOSITION". The '-explode' qualifier will increase the number of groups that the program belongs to by splitting the group name at selected points to produce such groups as: "NUCLEIC", "NUCLEIC COMPOSITION" and "COMPOSITION". All programs with the exploded group names which also include "NUCLEIC" and "COMPOSITION" will now be reported. The result of this qualifier is thus a report of a larger number of programs with a more tenuous link to the specified program. In other words, use the '-explode' qualifier to decrease the specificity of the search.
The groups that the program belongs to can be output by using the '-groups' qualifier.
% seealso Program to search for: matcher SEE ALSO 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
Mandatory qualifiers: [-search] string Enter the name of an EMBOSS program Optional qualifiers (* if not always prompted): -explode bool 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'. Using expanded group names will find many more programs which share at least some of the expanded names than using the non-exploded names and so you will get more programs reported as sharing a similar function than you will if you specify that you wish to use non-exploded names -outfile outfile If you enter the name of a file here then this program will write the program names and brief descriptions into that file. -html bool 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: http://www.uk.embnet.org/Software/EMBOSS/Apps/ programname.html then if you enter http://www.uk.embnet.org/Software/EMBOSS/Apps/ here, then the first half of the URL before the program name 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: http://www.uk.embnet.org/Software/EMBOSS/Apps/ programname.html then if you enter '.html' here, the second half of the URL after the program name will be set. -groups bool If you use this option, then only the group names will output to the file Advanced qualifiers: -[no]emboss bool 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 scheme, ie. they may wish to charge money for them. -[no]embassy bool 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 scheme, ie. they may wish to charge money for them. -colon bool The groups that EMBOSS applications belong to have 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 seealso 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. General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-search] (Parameter 1) |
Enter the name of an EMBOSS program | Any string is accepted | An empty string is accepted |
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'. Using expanded group names will find many more programs which share at least some of the expanded names than using the non-exploded names and so you will get more programs reported as sharing a similar function than you will if you specify that you wish to use non-exploded names | Yes/No | No |
-outfile | If you enter the name of a file here then this program will write the program names and brief descriptions into that file. | 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. | Yes/No | No |
-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: http://www.uk.embnet.org/Software/EMBOSS/Apps/ programname.html then if you enter http://www.uk.embnet.org/Software/EMBOSS/Apps/ here, then the first half of the URL before the program name 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: http://www.uk.embnet.org/Software/EMBOSS/Apps/ programname.html then if you enter '.html' here, the second half of the URL after the program name 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 | Yes/No | No |
Advanced 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 scheme, ie. they may wish to charge money for them. | 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 scheme, ie. they may wish to charge money for them. | Yes/No | Yes |
-colon | The groups that EMBOSS applications belong to have 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 seealso 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. | Yes/No | No |
If the '-html' qualifier is used, then the result is an HTML-formatted table, lacking the HTML document structures such as <HTML>, <BODY>, </BODY>, </HTML> which the user is expected to provide as the table will usually be included in the middle of a larger HTML document.
FATAL ERROR: No application specified.is output if a non-existent program name is specified.
Program name | Description |
---|---|
abiview | Reads ABI file and display the trace |
cirdna | Draws circular maps of DNA constructs |
infoalign | Information on a multiple sequence alignment |
infoseq | Displays some simple information about sequences |
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 |
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 |
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 |