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GENOMICS SOFTWARE


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CisOrtho logo

Transcription Factor Binding Site Prediction using Position Weight Matrices and C. elegans/C. briggsae Ortholog-based Filtering (Phylogenetic Footprinting)

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Circos logo

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. Although originally designed for visualizing genomic data, it can create figures from data in any field. It requires PERL software language.

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Integrative Genomics Viewer (IGV) logo

The Integrated Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations.

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BDPC DNA methylation analysis logo

BDPC, Bisulfite sequencing Data Presentation and Compilation, is an online DNA methylation analysis platform for analysis of primary bisulfite sequencing experiments, compilation and web display of methylation data, vlustering of methylation data from different samples

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GenePattern logo

GenePattern is a powerful genomic analysis platform that provides access to more than 150 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

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JaMBW 1.1 logo

JaMBW, the Java based Molecular Biologist's Workbench, is an online platform that had been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has. The peculiar aspect of JaMBW, however, is to take advantage of the foremost developments in computer science in order to deliver information in a way simple to use.

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Argo Genome Browser logo

The Argo Genome Browser is the Broad Institute's production tool for visualizing and manually annotating whole genomes. It's a free and open source standalone Java 1.4 application.

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Infernal logo

Infernal (inference of RNA alignments) is a software package for searching DNA sequence databases for RNA structure and sequence similarities. It allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments.

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BioQuery logo

BioQuery is a multi platform bioinformatics software program that provides a single, powerful user interface for building search strategies for numerous different biomedical databases.

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GERP logo

Genomic Evolutionary Rate Profiling (GERP) identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as "Rejected Substitutions".

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VAAST logo

VAAST (the Variant Annotation, Analysis and Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases.

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AltAnalyze logo

AltAnalyze is an easy-to-use application for microarry and RNA-Seq analysis. For splicing sensitive platforms, AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for conventional arrays (RMA summarization, QC, statistics, annotation, clustering, lineage characterization and gene-set enrichement).

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SMS Sequence Manipulation Suite logo

The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.

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MUMmer logo

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included wit

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SIFT logo

SIFT predicts whether an amino acid substitution affects protein function.

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Eisen Lab Microarray logo

All software for microarray analysis produced by Michael Eisen lab in the HHMI at UCB may be downloaded and used free of charge by academic and other non-profit researchers.

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Glimmer logo

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.

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PhageFinder logo

Automated Identification of Prophage Regions in Complete Bacterial Genome Sequences

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Sybil logo

Sybil is a web-based software package for comparative genomics. It was developed by the Bioinformatics department at The Institute for Genomic Research (TIGR) and development continues at the J. Craig Venter Institute and Institute for Genome Sciences (IGS) at the University of Maryland Baltimore's School of Medicine. The project has been funded by a variety of sources including: The National Institute of Allergy and Infectious Diseases (NIAID) as part of the NIAID Bioinformatics Resource Center

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PHAST logo

PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel).Like algorithms that assess protein-coding genes, they evaluate variants on the basis of how often the sequence changes between species

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