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ReadMe.txt
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ReadMe.txt
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===============================================================================
rasbhari 1.4.0 ReadMe by L. Hahn, August 2017, G.-A.-University of Goettingen
===============================================================================
CONTENT
#0 About rasbhari
#1 Extract tar-gz-file
#2 Requirements
#3 Compilation
#4 Run RasBhari
#5 Authors and location
#6 Copyright
#7 Thanks!
#8 How to cite
-------------------------------------------------------------------------------
0) About rasbhari
(Rapid Approach for Seed optimization Based on a Hill-climbing
Algorithm that is Repeated Iteratively)
rasbhari is a program that creates patterns/seeds for a user chosen
configuration for number of patterns, their weight and their length.
If the user wishes, rasbhari optimizes the variance or overlap
complexity of a patternset, which were generated automatically or were
read from a submitted patternfile.
It is also possible to calculate the sensitivity of a patternset and
tries to optimize the patternset to a higher sensitivity.
-------------------------------------------------------------------------------
1) Extract zip-file
Open the file containing folder and press right mouse-button, click
on 'Extract here...'.
-or-
Use the command line and move to the containing folder. Use the
following command to extract the archive:
$ tar xzfv rasbhari.tar.gz
-------------------------------------------------------------------------------
2) Requirements
To compile and run rasbhari an C++ IDE like GCC or Visual Studio / a
C++ compiler and the latest revision of C++ standard(2011), also known
as C++11 standard, is needed.
-------------------------------------------------------------------------------
3) Compilation
To compile rasbhari on Unix/Linux systems/derivatives, use 'make' for
the compilationafter changing into the RasBhari folder:
$ make
-or-
If you want to, or do not have make, you can manually compile rasbhari:
$ g++ -std=c++11 -O3 -Wall main.cpp rasbopt.cpp rasbimp.cpp rasbhari.cpp
rasbcomp.cpp sensmem.cpp speedsens.cpp patternset.cpp
pattern.cpp -o rasbhari
If you do not use the GCC-compiler, the term 'g++' might change!
-------------------------------------------------------------------------------
4) Run RasBhari
To run RasBhari please have a look at the command-help-file!
An example program launch could be:
./rasbhari -m 10 -w 8 -d 6-15 -H 64 --permut 25000
-------------------------------------------------------------------------------
5) Authors and location
This software/program was created by Lars Hahn at the George-August-
Universtiy of Goettingen.
----------
The ideas are from Burkhard Morgenstern, Lars Hahn and Chris-André
Leimeister at the George-August-University of Goettingen.
The following functions of the speedsens.cpp file:
- inline long long BIN_REVERSED_TO_INT2(char *s)
- double MULTIPLE_SENSITIVITY2(char** SEEDS, int NO_SEEDS, long long N, double P)
after the line with the speed comment, were created by Silvana and
Lucian Ilie in the software called 'SpEED'.
Therefore please have a look at:
Lucian Ilie, Silvana Ilie, and Anahita M. Bigvand. SpEED: fast
computation of sensitive spaced seeds. Bioinformatics, 27:2433–2434, 2011.
-------------------------------------------------------------------------------
6) Copyright
This software is created under the Terms of the GNU GENERAL PUBLIC LICENSE.
Therefore please have a look at the 'Copying' file!.
-------------------------------------------------------------------------------
7) Thanks!
A special thanks for Laurent Noé for pointing out a similarity between
the overlap complexity from Ilie & Ilie and the variance, and also for
some debugging for the first public run!
-------------------------------------------------------------------------------
8) How to cite
If you are using rasbhari for your own approaces, please cite us:
| Hahn L, Leimeister C-A, Ounit R, Lonardi S, Morgenstern B (2016)
| rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
| PLoS Comput Biol 12(10):e1005107. doi:10.1371/journal.pcbi.1005107