REDUCE 1.0 – Optimal Design of Gene Knock-out (KO) for the purpose of Gene Regulatory Network (GRN) Inference

REDUCE 1.0

:: DESCRIPTION

REDUCE (REDuction of UnCertain Edges) is an algorithm for finding the optimal gene KO experiment for inferring directed graphs (digraphs) of gene regulatory network (GRN).

:: DEVELOPER

Chemical and Biological Systems Engineering Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / windows/ MacOsX
MatLab

:: DOWNLOAD

REDUCE

:: MORE INFORMATION

Citation

Optimal design of gene knock-out experiments for gene regulatory network inference.
Ud-Dean SM, Gunawan R.
Bioinformatics. 2015 Nov 14. pii: btv672

Reduce 3.23 – Add Hydrogens to PDB Molecular Structure File

Reduce 3.23

:: DESCRIPTION

Reduce is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Windows with cygwin1.dll
Mac / Linux

:: DOWNLOAD

Reduce

:: MORE INFORMATION

Reduce is described in Word, et al.(1999) “Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation” J. Mol. Biol. 285, 1735-1747. ( PDF, 804KB)

MASon rev12 – Reduce the Computing Time of NGS Analysis Pipelines

MASon rev12

:: DESCRIPTION

MASon (Million Alignments in Seconds) is a C++ library that uses high performance architectures to reduce the computing time of NGS analysis pipelines.MASon employs an optimized SW implementation to align NGS reads and exploits graphic cards (CUDA, OpenCL) and CPU vector instructions (SSE, OpenCL). This allows computation of millions of short local pairwise sequence alignments (36bp – 1,000bp) within a few seconds. MASon can be easily integrated into NGS analysis pipelines and allows programmers to optimally utilize modern hardware, ranging from desktop computers to high-end clusters.

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MASon

:: MORE INFORMATION

Citation:

Rescheneder, P., von Haeseler, A., Sedlazeck, F. J.,
Mason: Million alignments in seconds,
In Proceedings of the International Conference on Bioinformatics: Models, Methods and Algorithms, 2012, Algarve, Portugal

FASTER 1.0 – Reduce Family Members for GENEHUNTER program

FASTER 1.0

:: DESCRIPTION

FASTER (FAmily SmarT EliminatoR)is to reduce family members so the families can be used in GENEHUNTER program. FASTER eliminates the most redundant individuals according to the set of weights (preferences) (Age, Information about genetic Markers, etc.) The program has several features such as automatical reducement of branches without any affected individuals, etc.

::DEVELOPER

Cyril Hoschl

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows/

:: DOWNLOAD

FASTER

:: MORE INFORMATION