Sequence Analysis
This list covers only a small selection of software applications that are available to UCR researches. If you are interested in additional tools, please contact 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.
Phred/Phrap/Consed [Manual]
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.
Tigr Assembler
An alternative assembly software is the TIGR Assembler.
GCG [Manual]
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:
- Command-Line
- SeqLab: graphical X-windows interface
- SeqWeb: web browser interface (http://gcg.ucr.edu)
All three applications are installed at UCR on the UNIX server cache.ucr.edu where they share the same sequence databases.
- Command-Line GCG and SeqLab: In order to use Command-Line GCG and SeqLab, you need to set up an account on cache.ucr.edu by emailing Terri McDonald (terri.mcdonald@ucr.edu) your user name and password. To run SeqLab from a PC, you need to open X-Win32 first and then connect from the PuTTY terminal via ssh (configuration). For Mac OS X we recommend using the new X11 terminal (configuration). The instructions on the environment settings for older MAC systems can be found on http://kansas.ucr.edu/exodus/. For an efficient file exchange between UNIX and your local computer, we recommend using WinSCP for PCs and fugu for Macs.
Help on using the different GCG programs can be found in the UCR SeqLab Manual or on the Accelrys help page.
- SeqWeb: The UCR license for SeqWeb was discontinued in spring 2006.
EMBOSS [Manual]
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 data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. For more information please read our UCR EMBOSS Manual.
BioPerl
The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.
Vector NTI
The Vector NTI license is free of charge for academic users. The software can be downloaded from the Invitrogen site.
Gene Prediction and Annotation
PHYLIP
PHYLIP is a free phylogeny package developed by Joe Felsenstein. Several manuals are available: Quick Guide and Complete Manual.
ARB
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:
- Start X-Win32
- Start terminal
- Provide user name and password
- Start the software with command "arb". To start demo, go to /home/arb/demo.arb.
Microarray/Chip Analysis
BioConductor [Manual]
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 data. All software components are freely available for all operating systems.
Affymetrix Suite
The following Affymetrix software packages are installed on two of our workstations:
- MAS 5.0 (image analysis tool)
- DMT (data mining software)
- MicroDB (database)
GeneSpring
Currently, we own one three-year license of the data mining software "GeneSpring". The software is available on one of our workstations.
BASE
BASE is a web-accessible database and data mining tool for microarrays and Affymetrix chips. It can be accessed via this UCR page.
Freeware
A huge number of excellent free software is available for microarray analysis. Many of these tools are available in our facilty.
Molecular Modeling
Insight II
Several modules of the 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.
GRASP
The molecular visualization and analysis program GRASP from the Honig lab runs on the same SGI workstation.
Prospect
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.
Chemical Genetics
Cerius2
Cerius2 is an analysis tools for chemical library diversification, sub-setting, descriptor generation and QSAR analyses.
Catalyst
Catalyst is an application for conformer generation of drug-like compounds, pharmacophore modeling and 3D database searching.
SciFinder
SciFinder allows substructure searches in literature. It is a local application.
ISIS Base
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.
CACTVS
CACTVS is a freely distributed collection of software and database applications for computational chemistry. This toolkit can also be downloaded from Xemistry.
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.
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