KBRIN BIOINFORMATIC CORE
Bioinformatics Software
Licensed
Software
Vector NTI AdvanceTM 9.1 (11/15/2004)
Vector XpressionTM 3.1.0 (4/15/2004)
Vector NTI® Suite 7.1 for Mac (OS X Panther) (3/31/2004)
Informax is now Invitrogen; the latest version can be downloaded from this site:
For a license and download instructions:
UofL Contact: Dr. Eric Rouchka
UK Contact: Rochelle Clinton
Vector XpressionTM 3.1.0 (4/15/2004)
Vector NTI® Suite 7.1 for Mac (OS X Panther) (3/31/2004)
Informax is now Invitrogen; the latest version can be downloaded from this site:
For a license and download instructions:
UofL Contact: Dr. Eric Rouchka
UK Contact: Rochelle Clinton
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.
(Available to members of the BRG only)
To create an account, contact Eric
Rouchka
Bioinformatics Utilities
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/
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/
iNquiry
A collection of commonly used bioinformatics software. It has been optimized for UK Apple G5 bioinformatics cluster and have a web portal for access.
• Location: UK BIGAPPLE server
• Web interface and command line access
A collection of commonly used bioinformatics software. It has been optimized for UK Apple G5 bioinformatics cluster and have a web portal for access.
• Location: UK BIGAPPLE server
• Web interface and command line access
GBrowse (part of GMOD)
Web-based feature browser. Visual display of the annotation of genomes
as well as other sequences through web interface.
•
Location: UK FUNGUS server
• Web interface
Software
Under Development
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/
Reseach Project
KBRIN BLAST Server
Locally installed web blast services based on NCBI-blast.
Interface: http://kbrin.a-bldg.louisville.edu/Tools/blast/blast.html
Locally installed web blast services based on NCBI-blast.
Interface: http://kbrin.a-bldg.louisville.edu/Tools/blast/blast.html
KBRIN BLAST Server
Locally installed web blast services based on NCBI-blast.
Interface: http://kbrin.a-bldg.louisville.edu/Tools/blast/blast.html
Miscellaneous
Software
DNA and protein sequence alignment:
- NCBI BLAST is a DNA and protein sequence alignment tool, allowing for multiple
sequence queries to be searched against a database of sequences.
• Location: UofL: NCBI Blast Home Page
UK: BIGAPPLE, GENOME, FUNGUS servers - WU-Blast is the Washington University version of BLAST, written by one of the original authors of BLAST. Local web WU-BLAST, site license approved, contact Dr. Eric Rouchka for access.
- MPI Blast 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/ - ClustalW-MPI is a parallel implemention of Clustal-W, based on MPI UofL: contact Dr. Eric Rouchka
- Miropeats
Miropeats is capable of genome scale sequence comparison and displays the results graphically in PostScript files. UK: Contact Rochelle Clinton - MUMMER
Fast alignment of large-scale DNA and protein sequences. UK: Contact Rochelle Clinton
Repetitive element structure
- 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 .
• Location: UofL RepeatMasker Home Page
UofL MaskerAid Home Page
UK GENOME server - RepeatFinder is a computational system for analysis of repetitive structure of genomic sequences. RepeatFinder requires Reputer to work. UK: Contact Rochelle Clinton
- REPuter computes and visualizes repeats in whole genomes or chromosomes. It uses suffix trees method. UK: Contact Rochelle Clinton
- RECON finds repeat families by BLAST search and clustering BLAST results.UK: Contact Rochelle Clinton
Motif Detection
- Gibbs Motif Sampler allows for the detection of multiple conserved regions called motifs within either DNA or protein sequences. Gibbs Motif Sampler Home Page
- MEME/MAST 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
- rnamotif
Sequence Assembly
- Phred/Cross_Match/Phrap/Consed - PHRED reads sequencer output files and "calls" the bases producing a text file with the sequence. Cross_Match screens the sequence against known vector sequences. PHRAP reads the PHRED/Cross_Match sequences and assembles the sequences into a contig. A script file called phredPhrap runs both programs in the appropriate order. CONSED is a GUI program which uses PHRED/PRAP output to create consensus sequences, provide for display of the sequencer traces and allow for editing. UK: Contact Rochelle Clinton
biojava; matlab; R; bioconductor; perl; bioperl; MySQL; StatServer and S+ArrayAnalyzer; StackPACK
Misc:
NWChem; jemboss;
primer3; modeller; Genesis; embassy
Institutional
Development