BIOLOGICAL SEQUENCE ANALYSIS
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BIOLOGICAL SEQUENCE ANALYSIS |
| Math/Stats 547 (Lecture) and 548 (Lab) | MWF, 9-10 (1084 East Hall); Fri, 10-11 (B743 East Hall) |
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| Entrez | The main database/server center at NIH |
| USC Comp Bio Group | Waterman Server. (SeqAln online manual) |
| Expasy | Home of SwissProt |
| SAM at UCSC | A suite of programs for HMM's. |
| HMMer online (Inst. Pasteur) | A suite of programs for HMM's. |
| Pfam at Washington Univ. |
Other sites in UK, etc. The most recent published description of Pfam. You can also access HMMer here, its home base for now. |
| GENSCAN at MIT |
This site includes a server for GENSCAN as well as a lot of useful documentation about limitations, etc. |
| HMMgene (Copenhagen) |
This site includes a server for HMMgene, trained for vertebrates and C. elegans. Not as much documentation. |
| Burset-Guigo Data Sets |
Useful data sets and their successors calibrating gene finders. |
| PHYLIP Phylogeny Programs |
A server supported by the Institut Pasteur, Paris.
Felsenstein commends them on their ``bravery",
since some of these programs are computationally intensive. (Click ``Phylogeny" to see Phylip.) |
PHYLIP and |
The first liink is to Joseph Felsenstein's PHYLIP home page. The second link is to a links page he maintains to access many other available phylogeny software options. The PHYLIP home site has very good documentation for all programs. |
| PDB | Protein Data Base |
| Workbench | Mainly structural tools |
| Search CPAN |
DB of Perl Modules for downloading; check, especially, BioPerl. NOTE: BioPerl 1.2 is available in the 548 resource directory. You can examine it in some detail there and download individual scripts you think you can use. For the full release, go through CPAN. |
| Kevin Murphy Software Distributions |
Download site for several Toolboxes (freeware)
Netlab (by Ian Dabney) -- a Neural Nets Toolbox HMM Toolbox Bayes Nets Toolbox Etc... |
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