Biol 591 |
Resources and Links |
Fall 2003
|
Links to useful sites
Links to useful protocols
and tables
Links to useful programs
Links to useful sites | |
Bioinformatics resources on web | Annotated list of web-based programs for analyzing DNA and protein sequences |
Meme | Discovers motifs within sets of unaligned sequences |
Molecular Toolkit | Colorado State's collection of useful tools to manipulate DNA and protein sequences |
NCBI | National Center for Biotechnology Information: Home of Blast, Entrez, much else |
Perl - Beginning Perl | Link to site dedicated to Beginning Perl, by Simon Cozens |
Perl - Documentation | Core documentation for Perl. Lots of stuff. |
Perl - Introduction | Short explanation of basic Perl features |
BioPerl | Repository of Perl code that bioinformaticians have found useful |
Protocols and Tables | |
Download Adobe Acrobat | You probably already have Acrobat on your computer, but if you can't read PDF files, try downloading a free copy. |
Genetic code | Useful on line reference to recall code, types of amino acids, and their abbreviations |
How to download Perl | You can use Perl on a server, but you might be happier having a free copy on your own computer. There will be some exercises where you'll NEED your own copy. |
How to write/run a program | Entering a program on your own computer and running it |
How to download Blast | Get a copy of Blast for your own computer, to run genomic comparisons or other applications you can't do through the web version |
How to download bacterial genomic databases | Access TIGR's set of completed bacterial genomes to download files containing complete list of proteins or complete DNA sequence |
How to set up a database for Blast | Create a database consisting of set of proteins or DNA sequence. Use this database later as a target for Blast searches. |
How to run Blast to compare genomes | Compare a set of proteins or DNA sequences to a local database. |
Useful programs | |
Perl template | An outline into which you can plug a Perl program |
DR | (read DRectory) - useful in reading through massive files. |