BIOINFORMATICS SOFTWARE AVAILABLE AT THE UNIVERSITY OF LOUISVILLE

Downloadable/Licensed Software

Vector NTI AdvanceTM 9.0 (9/9/2003) Vector XpressionTM 3.1.0 (4/15/2004) Vector NTI® Suite 7.1 for Mac (OS X Panther) (3/31/2004) These programs can be downloaded from Invitrogen's website: http://www.invitrogen.com/content.cfm?pageID=10225 Academic researchers in the state of Kentucky have access to the Dynamic License Server at no cost thanks to the Kentucky Biomedical Research Infrastructure Network (KYBRIN or KBRIN).  For more information on connecting to the DLS, contact Eric Rouchka (eric.rouchka@louisville.edu).

InsightfulTM S+ 6.2 S+ ArrayanalyzerTM 2.0 The University of Louisville Bioinformatics Research Group has a small number of dynamic licenses available through a windows server.  To create an account, contact Eric Rouchka (eric.rouchka@louisville.edu). (Available to members of the BRG only)

Web based Software

	Accelrys SeqWeb Version 2 Web interface for the Genetics Computer Group (GCG) Software package for nucleotide and protein sequence analysis.  For more information, see the web site: http://www.kbrin.louisville.edu/res-tools/gcg.html
	MPrime: Multiple Primer Design Locally developed program for the design of multiple primers or oligos, given a fasta sequence, GenBank or RefSeq ID, gene name, or keyword. Interface: http://kbrin.a-bldg.louisville.edu/Tools/MPrime/
	KyBRIN BLAST Server Locally installed web blast services based on NCBI-blast.   Interface: http://kbrin.a-bldg.louisville.edu/Tools/blast/blast.html
	emboss (European Molecular Biology Open Software Suite) Includes a wide variety of programs, ranging in application from dna and protein database searching to presentation of sequence data.   Two interfaces are available: http://kbrin.a-bldg.louisville.edu/EMBOSS/ http://kybrin.louisville.edu/EMBOSS/

Software Installed on Bioinformatics Cluster

(The majority of these programs can be found in the /bio/bin directory)
If a software package you are interested in using is not in this list, please contact: Eric Rouchka (eric.rouchka@louisville.edu)

	NCBI Blast BLAST is a DNA and protein sequence alignment tool, allowing for multiple sequence queries to be searched against a database of sequences.  BLAST stands for Basic Local Alignment Search Tool.   NCBI Blast Home Page: http://www.ncbi.nlm.nih.gov/BLAST/
	WU-Blast WU-BLAST is the Washington University version of BLAST, written by one of the original authors of BLAST.  WU-BLAST has some different default settings and some tweakings to the search algorithms that make it slightly different than the NCBI version. WU-Blast Home Page: http://blast.wustl.edu/
	MPI Blast "mpiBLAST is a freely available open source parallelization of NCBI BLAST. mpiBLAST segments the BLAST database and distributes it across cluster nodes, permitting BLAST queries to be processed on many nodes simultaneously. mpiBLAST is based on MPI." MPI Blast Home Page: http://mpiblast.lanl.gov/
	Gibbs Motif Sampler The Gibbs Motif Sampler allows for the detection of multiple conserved regions called motifs within either DNA or protein sequences.  The Gibbs Motif Sampler is based on a statistical technique called Gibbs Sampling, which attempts to avoid the problem of local optima by sampling from motif probabilities, rather than selecting the motif with the highest probability. Gibbs Motif Sampler Home Page: http://bayesweb.wadsworth.org/gibbs/gibbs.html
	RepeatMasker and MaskerAid These programs detect interspersed repetitive elements and low complexity regions in DNA sequences.  Native RepeatMasker employs a slower, more sensitive dynamic programming approach, while MaskerAid is built on top of WU-BLAST, making it much more efficient (approximately 30-fold faster). RepeatMasker Home Page:  http://www.repeatmasker.org/ MaskerAid Home Page: http://blast.wustl.edu/maskeraid/
	NWChem "NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. " NWChem Home Page: http://www.emsl.pnl.gov/docs/nwchem/nwchem.html
	emboss and jemboss Includes a wide variety of programs, ranging in application from dna and protein database searching to presentation of sequence data. emboss programs can be run either through the command line or via the jemboss java interface. emboss Home Page: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/
	MEME/MAST MEME is a motif detection program using expectation/maximization algorithms.  MAST is a program that will search databases for a particular motif. MEME/MAST Home Page: http://meme.sdsc.edu/meme/website/intro.html
	Various Other Programs Other bioinformatics related programs installed include: rnamotif, primer3, biojava, matlab, R, bioconductor, clustalw-mpi, gibbs sampler, modeller, phrap, Genesis, perl, bioperl, MySQL, embassy