|Thomas Girke. A general list on bioinformatics software and databases can be found on our link page. |
BLAST, FASTA and Smith-Waterman [Manual]
A wide variety of sequence and pattern search tools is available on our servers. Please contact us with your needs.
SAM and HMMER [Manual]
SAM and HMMER are pipelines for analysing gene families and identifying remote homologs.
The trace file editing, assembly and SNP analysis pipelines, Phred/Phrap/Consed and PolyPhred, are installed on our server. To set up an account, please email Thomas Girke. To get started, please read the instructions in the "UCR Phred/Phrap/Consed Manual". Additional documentation can be found on the Bioinfo Helpdesk page.
The Wisconsin Package GCG is a software suite that contains over 130 sequence analysis tools. The package was developed by the Genetics Computer Group in Madison and is now maintained and distributed by Accelrys. It can be accessed remotely from any networked computer. There are three different interfaces for accessing GCG:
The European Molecular Biology Open Software Suite (EMBOSS) is a new, free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with da
Gene Prediction and Annotation
ARB is a rRNA database, alignment & phylogenetic reconstruction software. It runs on our Bioinformatics Core server. Remote access via X-Win is possible. The instructions are given below:
The statistics software R and the associated BioConductor project have become the "golden standard" for the analysis of dual color microarrays and Affymetrix chips. The environment integrates the most advanced analysis tools that are currently available for profiling da
The following Affymetrix software packages are installed on two of our workstations:
Currently, we own on
BASE is a web-accessible database and da
A huge number of excellent free software is available for microarray analysis. Many of these tools are available in our facilty.
Insight II software from Accelrys are available on our SGI workstation. Currently we have Biopolymer, Sketcher, Modeler and the Affinity/Discover bundle. If you are intersted in using them, please email Thomas Girke. Remote access via X-Win is possible.
The molecular visualization and analysis program GRASP from the Honig lab runs on the same SGI workstation.
PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit) is installed on our Linux cluster. It is a threading-based protein structure prediction system. PROSPECT is designed particularly for the recognization of the fold template whose sequence has insignificant homology to the target sequence.
Additional Molecular Modeling Tools
Summary of Protein Modeling Workshop
The following overview provides links to the different exercises and tools that were used in our Protein Modeling Workshop on Nov. 8-9, 2002.
Cerius2 is an analysis tools for chemical library diversification, sub-setting, descriptor generation and QSAR analyses.
Catalyst is an application for conformer generation of drug-like compounds, pharmacophore modeling and 3D database searching.
SciFinder allows substructure searches in literature. It is a local application.
A simple but very useful compound database system with substructure search capabilities is ISIS Base from MDL (local application).
Currently we have loaded the following databases into ISIS Base:
Cambridge Structural Database (CSD)
ConQuest and Mercury are local application for querying the Cambridge Structural Database (CSD, 272,000 CMPs). They provide 3D structures and allow substructure searches.
SDF Toolkit in Perl 5
The purpose of the SDF toolkit is to provide functions to read and parse SDFs, filter, and add/remove properties. It can also read comma separated value (CSV) tables which contain new fields to be added to the SD file. A typical application is to retrieve chemical formulas, molecular weight and Log P values from SDF files.