TAIR -- The Arabidopsis Information Resources maintains a database of genetic and molecular biology data for Arabidopsis thaliana.
NCBI (National Center for Biotechnology Information) -- collection public databases for research in computational biology, genome data, and biomedical information.
Ensembl -- software system which produces and maintains automatic annotation on selected eukaryotic genomes.
GenePattern -- analysis workflow tool developed to support multidisciplinary genomic research program.
BLAST -- analysis tool that finds regions of similarity between biological sequences.
Bioinformatics.org -- Find computational resources and programs; online training in Computer Science, Computational Biology and Applied Math & statistics, established online community.
Star -- MIT's homegrown Software Tools for Academics and Researchers to support understanding and applying research methods in the classroom.
Online Bioinformatics Resource Collection (OBRC) -- Hosted by the University of Pittsburgh's Health Sciences Library System. OBRC is an extensive manually curated collection of biolnformatics databases and software tools (no longer updated).