UProC Version 1.2.0 2015-03-09 README
UProC uses semantic versioning. This means that the version number has the
MAJOR.MINOR.PATCH and an increment in one of the parts has the
MAJOR: The user interface (input, output and/or command-line arguments) of the programs or the format of the supplementary files was changed in a backwards-incompatible manner.
MINOR: Some functionality was added.
PATCH: One or more bugs were fixed.
PATCH are incremented, all modifications are
backwards-compatible. See the semantic versioning homepage for details.
The code for the UProC executables is available under the GNU GPLv3 (see the
COPYING file). However, most of the functionality is separated into a
library called libuproc, using the GNU LGPLv3 (see the
We currently offer binary packages for Windows XP and later, for 32 bit (i686)
and 64 bit (x86-64, also known as amd64) architectures. To install, just
download and extract the corresponding zip file. Currently there is no
graphical user interface, you need to run UProC from a PowerShell or
Please note that UProC is primarily developed for (and works best on) GNU/Linux.
UProC uses the GNU Autotools, so installation should work on any system that
has a POSIX compatible
make and a C99 compiler.
For additional features, UProC has the following optional dependencies:
- zlib (highly recommended)
- Used for On-the-fly
gzip(de-)compression of files. This is probably already installed on your computer, but you need to make sure that the development headers are also available.
- UProC uses OpenMP for parallelization, if the compiler suports it. The configure script automatically detects whether this is the case.
- Doxygen (for developers, version 1.8.0 or later recommended)
- If Doxygen is available, it wil be used to generate the the API documentation of libuproc (which is also available at the UPRoC homepage.
To install UProC from a source tarball, simply extract it and run the commands
./configure make make install # requires appropriate privileges in PREFIX (see below)
By default, the executables are built in a way that you can omit the
install step and just run them from wherever you wish or copy them to a
desired location (it is recommended to utilize the
mentioned below, though).
You can pass the following options (and more) to the
|Install all files below |
|Do not use OpenMP (i.e. disable multi-threading). This will usually cause longer running times. You probably don't want this.|
|Link all execututables statically and do not build and install libuproc as a shared library.|
|--enable-mmap||Enable the |
INSTALL file for a more detailed description of the installation
process for projects using GNU Autotools.
On a fresh clone of the git repo, run
autoreconf -i to generate the
configure script and then follow the instructions in the previous section.
UProC needs certain files at runtime. These files are split into two categories, usually available as two distinct directories in the file system.
The database consists of files representing a set of known protein subsequences that map to given families, e.g. extracted from PFAM.
There are two ways to obtain a database:
- You can download a database from the UProC homepage and import it with
- Alternatively, you can create your own database with the
Detailed instructions for these programs can be found by passing the
option when running them.
The model consists of files containing certain parameters that are not tied to a particular database. You can download the newest model files from the UProC homepage.
UProC consists of the following command-line programs:
- Protein sequence classifier.
- DNA/RNA sequence classifier.
- Command-line interface to the ORF translation mechanism used by
- Import database.
- Export database.
- Create a new database.
You can pass the
-h option to find out how they are used.