A:

Rice P., Longden I. and Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics. 2000 16(6):276-277

A:

Yes. Here is the information you will need. Make sure you have cvs on your system. Then log into the cvs server at open-bio.org as: user cvs with password cvs.

The password is cvs To checkout the EMBOSS source code tree, put yourself in a local directory just above where you want to see the EMBOSS directory created. For example if you wanted EMBOSS to be seen as /home/joe/src/emboss... then cd into /home/joe/src then checkout the repository by typing:

Or if you want to update a previously checked-out source code tree:

You can logout from the CVS server with:

This is a read only server.

A:

If this is the first time trying to compile all you need to do is:

The above will produce the EMBOSS programs in the emboss subdirectory and you can set your PATH variable to point there. This method is suitable for EMBOSS developers. For system-wide installations we recommend installing the EMBOSS programs into a different directory from the source code (e.g. in the directory tree /usr/local/emboss). To do this type (e.g.):

You should then add (e.g.) /usr/local/emboss/bin to your PATH variable:

If you wish to re-compile the code at any stage then you should type make clean and then configure and make source again as appropriate.

A:

This should not happen with versions of EMBOSS later than 6.1.0 as the configuration will inform you of missing files and terminate at that stage. If you have a version of EMBOSS less than or equal to 6.1.0 then the problem is that you probably have the X11 server installed but you haven't installed the X11 development files. For example, on RPM distributions, you need to install:

After installing those system files you will need to:

and re-perform the ./configure command from the top EMBOSS source directory.

A:

Your system will need to have zlib (http://www.zlib.net: current version is 1.2.3), libpng (http://www.libpng.org: current version is 1.2.35) and gd (http://www.libgd.org: current version is 2.0.35). The version of gd must be >= 2.0.28 if it is to be used with EMBOSS.

Note that the above packages often come with your operating system distribution but may not be installed by default i.e. they are optional packages which you can install at a later date. Also note that, as well as having the above system libraries installed, you must also have installed their associated development files (these typically have devel in the package names on Linux systems). So, on Linux RPM systems you would need to make sure that packages called names similar to gd and gd-devel are installed.

MacOSX users can often find the above packages available on the MacPorts site (http://www.macports.org). However, for some operating systems, there may be no freeware sites where you can find pre-compiled versions of zlib / libpng / gd and you may have to compile one or more of them from their source distributions (URLs given above).

You can unpack the tar.gz or tar.bz2 files in any directory, and install them in a common area. By default everything (including EMBOSS) installs in /usr/local. To install, pick up the sources and then:

To compile with the local version your EMBOSS ./configure line should now read:

A:

There are the

and

flags. Did you try them? If the libraries are in /opt/png/lib then set dir to /opt/png i.e. one level above the lib directory.

A:

You will need automake, autoconf, (GNU) make and libtool for this. The gcc compiler is recommended. The host cc compiler should work. (Note that some non-gcc compilers may need --include-deps added to the automake command line.)

If you have system versions of the GNU tools that, by chance, are more recent than the GNU tools used in the EMBOSS source tree then typing autoreconf -fiv may be necessary before you start. MacOSX CVS users should also use autoreconf -fiv after downloading the source. Then type:

For more info on the configurability of the build try

A:

Here is how to install PHYLIP given the various ways you can install the main EMBOSS package.

From the anonymous cvs code.

From PHYLIP-3.68.tar.gz available from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file PHYLIP-3.68.tar.gz

If you have done a full installation of EMBOSS using a 'prefix' e.g. you configured with ./configure --prefix=/usr/local/emboss and followed this with a make install (highly recommended) then:

If, on the other hand, you did not do a make install of EMBOSS then:

A:

It is inside the binaries. EMBOSS 'knows' the location of the files because it is picked up during the configure, when you build your copy, and included in the binaries. You can see it during compilation, especially of ajnam.c (where it is used):

To copy binaries, you need to define environment variable(s) to override the compile-time definitions, unless you can make the path (e.g. /usr/local) the same for the installations at each site.

emboss.default can set environment variables too, but you need to tell EMBOSS where to find that file.

and then, in the emboss.default file you can set:

or (this overrides it) you can use another environment variable:

A:

If you have SRS installed (so you have local SRS index files) you will have a local copy of the getz program, which is part of SRS.

If you do not have SRS, you can build your own index files using dbxflat, dbxgcg (if you have GCG), dbiblast (if you have BLAST) and dbxfasta. This is the usual solution for sites that have no other database indexing in use.

You can also use SRS servers remotely, to get single entries, using their URLs. No extra software is needed (EMBOSS just uses the HTTP protocol). Of course, if you really need to build your own SRS indexes you could install it. SRS is a commercial product, but academic licences are available.

A:

This most often happens when using GNU LD. If both shared and static versions of a library exist then GNU LD will take the shared library as preferred. The root of this problem is libtool. You can, however, force complete static images by adding a definition to your "make" line:

A:

In the directory /emboss/emboss/test.

A:

You may wish to amend one of the standard EMBOSS data files. Some of the data files you might wish to alter are the translation table files. transeq has been written to only read in one of the standard translation files:

These files are the only ones that you can specify to transeq.

If you wish to create your own specialised translation table, then you should pick one of them to amend. For instance you may decide that you will use the file EGC.15 as you would never want to otherwise use it. Use the program embossdata to get a copy of this file:

% embossdata -fetch -filename EGC.15
Finds or fetches the data files read in by the EMBOSS programs
File '/fu/bar/emboss/data/EGC.15' has been copied successfully.

Edit the file EGC.15 to suit your requirements. Specify -table 15 when you run transeq to use this altered file. transeq will then look for the file EGC.15 and will find it in your current directory before it finds the default one in the EMBOSS_DATA directory. It will therefore use your local copy.

You may get confused with many copies of changed files floating about. To check which copy of a file is being used (the default EMBOSS_DATA one or a potential local copy) use embossdata:

%embossdata -filename EGC.15
Finds or fetches the data files read in by the EMBOSS programs
# The following directories can contain EMBOSS data files.
# They are searched in the following order until the file is found.
# If the directory does not exist, then this is noted below.
# '.' is the UNIX name for your current working directory.

File ./EGC.15                                            Exists
File .embossdata/EGC.15                                  Does not exist
File /home/joe/EGC.15                                    Does not exist
File /home/joe/.embossdata/EGC.15                        Does not exist
File /usr/local/emboss/data/EGC.15                       Exists

This shows that a copy of EGC.15 exists in your current directory and so will be used in preference to the default one in the EMBOSS_DATA directory.

A:

EMBOSS will find the ACD files in the install directory or in the original source directory (depending on how you configured it) so there is usually no reason to change this. However, should you wish to do so then it can either be done in the emboss.default (or ~/.embossrc) file:

or by setting an environment variable on the command line:

A:

EMBOSS does not cover the sort of contig assembly you describe. An EMBOSS wrapper for the MIRA package is available.

A:

EMBOSS is not good at writing multiple sequences to different files. You could try using nthseq to pull out one sequence at a time. You should consider using the -ossingle qualifier. This writes sequences to separate FASTA files, but the file names depend on the sequence ID. This is rarely used. It is there because -ossingle is the default for GCG output format. The output filename is currently ignored when ossingle is used, and the filename depends on each individual sequence.

A:

Tens of them(e.g.): gcg, embl, swissprot, fasta, ncbi, genbank, nbrf, codata, strider, clustal, phylip, acedb, msf, ig, staden, text, raw, asis etc.

A:

TEXT accepts everything in the sequence file as sequence. RAW accepts only alphanumeric and whitespace characters and rejects anything else.

A:

The "filename" is really the sequence. This is a quick and easy way of reading in a short fragment of sequence without having to enter it into a file. For example:

A:

For many sequence formats there is no way to specify the sequence type in the file, so EMBOSS has to guess. There is a flag that can force EMBOSS programs to treat sequences as nucleic or protein.

shows the full list of sequence qualifiers.

If you follow the sequence USA with -sprotein EMBOSS will check that it is a valid protein sequence and then treat it as such. If you need to force a sequence to be DNA, the qualifier is

The qualifier must follow the sequence to apply to one sequence, or can go at the start of the command line to refer to all sequences, for example:

You can also use -sprotein1 anywhere on the command line to refer to the first sequence and -sprotein2 to refer to the second sequence. Of course, like all EMBOSS qualifiers, you can shorten them so long as they are still unique. In this case, -sp and -sn will work (or -sp1 and -sp2 if you need the numbers.

A:

Mail emboss-bug@emboss.open-bio.org

A:

Rather than email their personal addresses, for EMBOSS matters we request that you use the address:

This will ensure that your email will be seen by the appropriate developer and that it will get logged with our tracking system.

A:

is an open list (anyone can join) for general announcements and discussions by users.

is a closed list (subscription requests have to be approved) for discussions by developers using EMBOSS.

is an open list for announcements of new releases.

You can access the archives, subscribe/unsubscribe and alter the way email is sent to you (e.g. digests) by visiting:

A:

See the EMBOSS tutorial in the EMBOSS Users Guide:

A:

All the documentation can be found at:

A:

http://emboss.open-bio.org/rel/dev/apps/ and in the EMBOSS distribution, installed under

You can also use the EMBOSS application called tfm to display the plain text documentation of another application e.g.:

A:

There is a dated quick guide provided with the source code as the file doc/manuals/emboss_qg.pdf. A postscript file is also available. However, the primary source of up-to-date information is the web site. The quick guide was not written by the EMBOSS team and it is therefore not maintained by them.

A:

A list of GCG and corresponding EMBOSS applications is available in the EMBOSS Users Guide:

A:

That is the correct answer. Instead of 3.6 residues per turn, (5 turns in 18 steps) you seem to have a helix with 8 turns in 18 steps (4 in 9). Try

but only if you are sure that is the way your helix goes.

A:

Creates prettyplot.ps The name is generated automatically. To set this to something more descriptive use -goutfile i.e.

Creates hello.ps

A:

Use Control-Z to get into command mode. Then use the SAVE command which will prompt for the file name.

A:

You can read any sequence type that EMBOSS can handle.

A:

The associated software will use the EMBOSS ACD files so the naming of output/input files is taken care of and will check all values before the program is run. Command line arguments are used instead interactive menu based ones.

A:

Every EMBOSS and EMBASSY program has an ACD (AJAX Command Definition) file which describes the application, its options (parameters) and command line interface. The ACD file controls the behaviour of the application at the command line, particularly, all the user input operations. It includes an application definition (describing the application itself), a data definition for every application option (which describe the program parameters), attributes of the data definitions and the datatype of each option.

A:

The EMBOSS command line is the simplest and best supported way to launch applications. The command line behaviour is consistent across all applications and provides a simple interface to (and complete control over) them. There are also web interfaces, graphical user interfaces, workflow various other types of interface. These simplify, at least for some people, the ways to run EMBOSS applications.

A:

To see what graphics drivers are available type ? at the prompt for the graph type and this will give you a list. Here are some of those:

A:

The hp drivers presume the pens are loaded as:

Otherwise your output will have different colours.

A:

So far they are still GPL licensed rather than LGPL. Robert Maier promised a while back to LGPL them but has not yet. A pity as it makes all the difference for linking in third party applications to EMBOSS.

A:

This should only affect versions of EMBOSS pre-5.0.0. The Hummingbird Exceed X11 emulator (and maybe other systems) use the 'TrueColor' display by default. You should change the configuration settings so that it uses 'PseudoColor'. In version 6.1 of Hummingbird Exceed, this is done by clicking on the Exceed section of the Windows 98 tool bar at the bottom of the screen. Select Tools, then Configuration, then Screen Definition. A window will appear. In the 'Server Visual' popup menu on the left, select PseudoColor. Click on OK.

A:

The maximum size for any program depends only on how much memory your system has. Of course, some programs (and some program options) can take up too much memory, or simply run very slowly. You might have a constraint imposed on your usage of memory. Try using the Unix command limit to look at such constraints. Try using the Unix command unlimit or ulimit to remove the constraints, eg:

A:

No. The mse package has no limit, you are only limited by how much memory you have.

A:

Just put these at the top after your use CGI ( whatever) statements.

These two are important, but you can also pass other "constants".

A:

Mail the EMBOSS developers at emboss-bug@emboss.open-bio.org