presented jointly by the Health Sciences Library and ACHS
2007 dates - November 28th, December 5th, 12th, 19th, respectively
I. WWW Resources for Molecular Biologists
II. Genetic Database Searches - BLAST & FASTA
III. Advanced BLAST Searches
IV. Clinical Genetics Resources
URL's from the ACHS/HSL special course "WWW Resources for Molecular Biologists"Windows users - download (right-click, "save target as") this file and import into your browsers Favorites/Bookmarks folder
(Internet Explorer will import the bookmarks to a favorites folder named "Mol Biol WWW Res 2006", as well as creating an empty folder named "Bookmarks Toolbar Folder" Other browsers, eg. Firefox, may not create the empty Toolbar folder).Mac users - download (control-click, "save link as") this file and import into your browsers Favorites/Bookmarks folder
(Users of Apple's Safari browser will need the free utility, TinkerTool, to enable the Safari debug menu which then allows importing of bookmarks. Safari will place the folder "Mol Biol WWW Res 2006" into a folder named "imported mm/dd/yy". Other browsers (eg. Firefox, Camino, Opera) may or may not also make an empty "Bookmarks Toolbar Folder" or "Bookmarks Bar" folder).
Notes for the BLAST & FASTA tutorial session - PDF format
References for Advanced BLAST Searches (available online through the Health Sciences Library)
PSI-BLAST:
Trends in Biochemical Sciences. Vol. 23(11), November 1998
Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases, Pages 444-447
Stephen F. Altschul and Eugene V. KooninTrends in Biochemical Sciences. Vol.27(3), March 2002
Getting the most from PSI-BLAST, Pages 161-164
David T. Jones and Mark B. SwindellsJournal of Molecular Biology. Vol.287(5), April 1999
Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches1, Pages 1023-1040
L. Aravind and Eugene V. Koonin
PHI-BLAST
Nucleic Acids Research. Vol.26(17), September 1998
Protein sequence similarity searches using patterns as seeds, Pages 3986-3990
Z. Zhang, A. A.Schäffer, W. Miller, T. L. Madden, D. J. Lipman, E V. Koonin, and S F. Altschul
rules for PROSITE pattern syntax
Classes: list of scheduled classes, including course descriptions. Courses are run throughout the year and are available at no cost to researchers at UVa. The classes are usually full, so remember to call for a reservation.
Individual Instruction
For researchers and students who require individual instruction or need to discuss specific research needs, please call me or send e-mail (mblack@virginia.edu) for an appointment.
Databases
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We maintain a large number of local databases.
Special databases can be installed and integrated with our software when necessary.
Custom Programs
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When commercial programs are not available, or when it may be more efficient
to automate analysis for a long-term project, custom programs can be written
or commercial programs can be adapted to address your specific needs.
Projects
For major sequencing, database mining, or phylogenetic analysis projects where faculty or researchers need active participation to analyze sequence data it is possible to set up a cooperative project. In such cases time would be set aside for the project and we would work on it as collaborators.
Please contact Michael Black (mblack@virginia.edu) for more information.
Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.
Academic Computing Health SciencesBox 800555
Charlottesville, VA 22908
(434) 982-4025