Data File Formats (University of California Santa Cruz)
The UCSC Genome Browser website contains the reference sequence and working draft assemblies for a large collection of genomes. The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering at the University of California Santa Cruz (UCSC).
DNA Subway (University of Arizona)
DNA Subway is a collaborative workspace to generate DNA sequence annotations, conduct phylogenetic analyses and analyze Next-Generation Sequencing data. It's an intuitive interface that uses the metaphor of a network of subway lines to guide users through the maze of analysis steps necessary to annotate and compare DNA sequences. Developed with an eye to undergraduate education, DNA Subway can make high-level DNA analysis available to faculty and students by simplifying annotation and comparative genomics workflows.
GenSAS - Genome Sequence Annotation Server (Washington State University)
The Genome Sequence Annotation Server (GenSAS) is an online annotation tool that provides a customizable automated pipeline for whole genome structural annotation. Users can upload genomic sequences and select from a variety of tools for prediction of gene models and other structural features.
Glossary of Terms (Davidson College)
A comprehensive glossary of terms related to the Biotech GPS program developed as part of Dr. Malcolm Campbell's genomics laboratory course at Davidson College.
IGB - Integrated Genome Browser (UNC Charlotte)
Next-generation sequencing technologies are making it much easier for individual labs to produce huge volumes of short- and long-read sequencing data. To get maximum value from these data, you often need to view the sequence reads alongside all the other known features in a genome. Using tools like BowTie and TopHat, you can align your reads onto a reference genome and then use IGB to view the alignments alongside canonical gene models provided by organizations such as The Arabidopsis Information Resource. IGB can read and display short read alignments from BAM files, the binary equivalent of SAM (Sequence Alignment/Map format) files output by many alignment tools.
National Center for Biotechnology Information (NCBI)
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. NCBI provides a variety of Tools for analyzing genomic data as well as Downloads to get NCBI data or software.