AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.
Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.
The Berkeley Phylogenomics Group provides a series of
web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.
The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.
BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.
CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.
CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.
COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.
The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
454 Databases
