Introduction to Bioinformatics - COIN81
Welcome to COIN81, Introduction to Bioinformatics. This course will introduce you to bioinformatics tools and databases available through the World Wide Web. This course meets "online" in Spring Qtr. 2009, with occasional seminars. Please feel free to contact me by email with comments / suggestions before the official (online) start of this course in April 2009. The course syllabus (pdf), outline, and tentative assignments can be accessed from this page.
Key sites and tools for review in this course.
NCBI - NCBI National Center for Biotechnology Information, which includes GenBank, PubMed, and BLAST, and many other great resources.
GenBank - GenBank contains over 15 million genomic records, many with corresponding protein records, and links to other NCBI data.
PubMed - PubMed is the "public" version of Medline, and a great source of medical, biological, and other reference information.
BLAST - Basic Local Alignment Search Tool for nucleotides, proteins, and the translated databases (BLASTx, tBLASTn, and tBLASTx)
Entrez Gene - provides a single query interface to curated sequence and descriptive information about genetic loci.
UniGene - UniGene is an experimental system for partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.
OMIM - Online Mendelian Inheritance in Man
HomoloGene - HomoloGene is a resource of curated and calculated orthologs for genes as represented by UniGene or by annotation of genomic sequences.
NCBI Structure - maintains MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis
Swiss Prot - SWISS-PROT Protein knowledgebase TrEMBL Computer-annotated supplement to Swiss-Prot
InterProScan - InterProScan Sequence Search (part of EMBL-EBI)
PIR - Protein Information Resource
Pfam
- Protein families database of alignments and HMMs
PDB - Worldwide repository for the processing and distribution of 3-D biological macromolecular structure data
ENSEMBL - ENSEMBL Genome Browser
UCSC Genome Bioinformatics - This site contains the reference sequence for the human and C. elegans genomes and working drafts for the mouse, rat, C. briggsae, and SARS genomes, the UCSC genome browser, and BLAT.
GeneCards - Database of human genes, their products and their involvement in diseases
GeneLynx - A one-stop shop for everything related to a gene. It is hyperlinked to every key bioinformatics database on the Web.
Biology Workbench - A Web based interface to an entire suite of bioinformatics tools housed on a UC San Diego super computer.
GenomeNet - Bioinformatics Center, Institute for Chemical Research, Kyoto University
Pathway Searcher - text search both BioCarta and KEGG pathways from the NCBI portal.
BioCarta - BioCarta pathways linked from NCBI Cancer Genome Anatomy Project.
KEGG - Kyoto Encyclopedia of Genes and Genomes (KEGG), Standard Pathways linked from NCBI Cancer Genome Anatomy Project.