Available upon request

RNAmmer

RNAmmer is software for predicting ribosomal RNA in full gene sequences.

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the RNAmmer group. The use of RNAmmer at MSI is limited to academic researchers.

TMHMM

TMHMM is software for the prediction of transmembrane helices in proteins.

 

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the TMHMM group. The use of TMHMM at MSI is limited to academic researchers.

SignalP4

SignalP4 is software for predicting the presence and location of signal peptide cleavage sites in amino acid sequences in different organisms.

 
To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the SignalP4 group. The use of SignalP4 at MSI is limited to academic researchers.

GeneMark-ET

GeneMark is the name of a set of gene prediction programs developed at the Georgia Institure of Technology. Genemark-ET is a member of this set of software for semi-supervised analysis of novel genomes.

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the GeneMark group. The use of GeneMark at MSI is limited to academic researchers.

 

 

USEARCH

USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

Spotfire

TIBCO Spotfire is no longer offered at MSI

The license to Spotfire expired Jan 1, 2016 and will not renewed.

 

IPA - Ingenuity Pathway Analysis

Ingenuity Pathways Analysis (IPA) is a software and database search tool for finding functions and pathways for specific biological states. It is a web-delivered application that makes use of the Ingenuity Pathways Knowledge Base, a currated database consisting of millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. It currently has data for humans, rats, and mice.

Vasp

Vasp is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in Vasp is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.
 

MacVector

MacVector is a sequence analysis software for Macintosh computers. It provides sequence editing, primer design, Internet database searches, protein analysis, sequence confirmation, contig assembly capabilities, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a wide variety of other functions.

 

Notice to users:

Though still available for access MacVector will no longer be updated after 10/2014.   

Scaffold Q+ for Proteomics

Scaffold is a computer program that integrates search results from search algorithms such as Sequest, X!tandem ,Mascot, Phenyx, OMSSA and Spectrum Mill to generate peptide identification and protein identification probabilities. Scaffold also displays an overview of the protein identifications for each search algorithm so that spectral identifications can be compared and validated by probability scores. Protein information can also be used to detect false positives and also examine the peptide and spectral evidence used for identification.

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