Bioinformatics Resources

BIOINFORMATICS RESOURCES

Animated Teaching Tools and Tutorials

Geospiza's Green Arrow Tutorials	Tutorials on BLAST, SNPs, Entrez, Protein Structure, Mitochondria, and others
DNA Interactive	Movies and interviews about DNA and genomic sciences

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins
Andreas Baxevanis and B.F. Francis Ouellette, John Wiley & Sons, 2005

Phylogenetic Trees Made Easy
Barry Hall, Sinaur Associates, 2001

Song of the Dodo
David Quammen

Tears of the Cheetah
Steven O'Brien

The Seven Daughters of Eve
Brian Sykes

ABIM	A collection of well-organized links to tools for working with sequences and databases
Baylor College of Medicine Search Launcher	A very handy collection of links to tools for working with sequences. Examples are tools that provide the reverse complement of a sequence, change the sequence format to FASTA, translate a sequence in all six reading frames.
GeneTests	A publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers
MultiAlin	A quick tool for multiple alignments
National Center for Biotechnology Information	There are many tools at NCBI. These include BLAST, COGS, ENTREZ, ORFFINDER, Cn3D, and lots of others.
Nucleic Acids Research Web Server Issue	This issue contains peer-reviewed articles on free web-servers running a variety of bioinformatics programs. Links to the servers are found in the abstracts of the articles.
Oligonucleotide properties calculator	A form for calculating Tm under different conditions, MW, and complementarity
Phylogeny programs	A well-organized, long list, links, and descriptions for 193 phylogeny programs and 18 free web servers.
Primer3	A web site for designing primers
UCSC Genome Browser	See how many different kinds of features map to your chunk of genomic DNA. Be careful about using the DNA feature since there can be mistakes.
VISTA	Tools for comparative genomics

BioCarta	A database of biochemical pathways with very nice drawings and lots of information.
Barcoding life	Lots of sequences and info that would be good for phylogeny studies
The Protein Data Bank (PDB)	PDB is the first bioinformatics database. Researchers all over the world submit three dimensional structure data from macromolecules to PDB.
MitoMap	A human mitochondrial database
National Center for Biotechnology Information	Several famous databases are housed at the NCBI. These include: GenBank, dbSNP, EST, MMDB, OMIM, PubMed, Taxonomy, TraceArchive. Many of the databases can be queried simultaneously with Entrez.
Nucleic Acids Research	This journal has annual database and web server issues that are great. The issules include references, descriptions, and links to databases on all aspects of molecular biology. Some examples in this list are databases on comparative genomics, mutations, pathology, RNA sequences, metabolic pathways, and structure.
Seattle SNPs	SNPs data mapped to several genes
GeneSNPs	more SNP data with nice tables
TreeBASE	TreeBASE is a relational database of phylogenetic information. Search and view phylogenetic trees.

Clustal	Programs for creating multiple alignments.
	Clustal Windows version click: ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ Double click clustalx1.8.msw.zip to download and unzip
FinchTV	A program for viewing chromatogram data Mac, Windows, Linux, and Unix versions are all available from this site.
Phylip	A collection of programs with several different methods for creating phylogenetic trees Mac, Windows, Linux, and Unix versions are all available from this site.
NJ plot	A user-friendly program for viewing phylogenetic trees.
	NJ plot _ Windows Version
RepeatMasker	A program for locating, identifying, and, if desired, hiding repetitive elements. This is often used in conjunction with BLAST searches.

DOE Primer on genomics and the genome project	A classic, well-written, reference, updated in 2003, that provides an overview of the genome project and defines many of the terms. If you don't know what ESTs, STSs, or contigs are, this is a great place to begin.
How to make a phylogenetic tree	This reference comes from the Los Alamos National Laboratory HIV sequence database. It includes a very nice discussion of tree-building methods along with some great diagrams that show common mistakes in preparing trees.
Nature's Genome User's Guide	A nice guide to using genome resources.
NCBI handbook	An overview of resources at NCBI.
University of Washington tutorials on genome sequencing	This site has a very nice set of guides to sequencing, analyzing genome sequences, and definitions, tools, and protocols.