Scripps Genome Center  

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The Scripps Genome Center provides guidance, resources and access to cutting-edge bioinformatics tools. We install, configure and maintain all of the software, allowing researchers to spend their time running experiments instead of managing software.

We continually monitor and analyze software developments, such as updates to current programs and releases of new software, to ensure that Scripps researchers have access to the best tools available. Our programmers work with the researchers to develop customized applications to fill the gaps left by standard tools.

Some of the major applications available are:

  • BLAST (Basic Local Alignment Search Tool) - a web-based tool to find regions of local similarity between sequences
  • Comprehensive Microbial Resource (CMR) - a web-based tool used to display information on complete prokaryotic genomes
  • EMBOSS (European Molecular Biology Open Software Suite) - a free Open Source software analysis package specially developed for the needs of the molecular biology user community
  • MAGPIE (Multipurpose Automated Genome Project Investigation Environment) - a web-based tool to identify genomic features within regions of the input sequence and construct static logical models of molecular systems from the features encoded in the genome
  • Manatee - a web-based gene evaluation and genome annotation tool that can view, modify and store annotation for prokaryotic and eukaryotic genomes
  • Sequencher - desktop tools to perform DNA sequence editing, contig assembly, restriction mapping and other common bioinformatics tasks
Use the links below to discover some of the other programs we support.

Enzyme Kinetics Protein Structure - Secondary Sequence Annotation and Features
Hidden Markov Models Protein Structure - Tertiary Sequence Assembly
Microarrays Publication Quality Display Sequence Composition - Nucleic Acid
Motif Searches - Nucleic Acid Sequence Alignment - Global Sequence Composition - Protein
Motif Searches - Protein Sequence Alignment - Local Sequence Editing
Nucleic Acid Secondary Structure Sequence Alignment - Multiple Sequence Homology
Phylogeny Sequence Alignment Dot Plots Sequence Mutation
Profile Generation and Searching Sequence Analysis
University of California, San Diego