NOTE: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 9/28/2017. If you need this software, please contact email@example.com . A software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach.
Amira is a powerful, multifaceted 3D software platform for visualizing, manipulating, and understanding biomedical data coming from all types of sources and modalities.
From the DIAMOND website: "DIAMOND is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity."
LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
The MEME/MAST is software system used for discovering motif (highly conserved regions) in groups of related DNA or protein (MEME) and searching sequence databases using motifs (MAST).
T-Coffee is a versatile tool for making multiple sequence alignments. Its aim is to combine heterogeneous sources of information. The current implementation has been especially designed for combining local and global alignments, respectively from ClustalW and Lalign. It can also be used to combine a series of alternative multiple sequence alignments of the same sequences.
Globus is a data transfer service designed for convenient, fast file transferes between computer systems. More information about using Globus on MSI can be found here . These command line tools provide an alternative interface to the Globus functionality.
From the GNU website: "The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite."
Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 12/20/17. If you need this software, please contact firstname.lastname@example.org . GraphClust can be used for structural clustering of RNA sequences. Especially it can be used for clustering of very large dataset with thousands of RNAs. http://www.bioinf.uni-freiburg.de/Software/GraphClust/
Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 12/20/17. If you need this software, please contact email@example.com . Goby is a next-gen gene sequence data management framework designed to facilitate the implementation of efficient data analysis pipelines.