Tools for Biochemists and Molecular Biologists

Some of these programs allow for submission of user data, and produce GIFand/or postscript files in returned results. For best use of these facilities,configure your system to use GSView for viewing postscript files, have accessto an image editing system to manipulate and/or translate GIF images, andconfigure your browser to launch RasMol for MIME type chemical, subtype x-pdbfiles and Kinmage for MIME type chemical, subtype x-kin files.

You may want to examine the relevant information and exercises that I compiledfor a computer classin the Fall of 1995.

Multiple Sequence Alignment via ClustalW
Analysis of E. coli genome sequences

EcoSeq - gene functions, motifs and clusters identified using individual sequences and alignment blocks.
GeneMark - Three gene classes, defined by factorial correspondence analysis and dynamic clustering methods. (The GeneMark programs GM5_ECO1 and GM4_ECO3 are also available via an Email server.)

SEQSCAN - Site Identification in DNA Sequences

Using a pre-defined scoring matrix
Preparing a user-defined scoring matrix
The Ihf / s54-promoter example

Amino Acid Sequence Analysis (molecular weight, apparent specific volume, extinction coefficient, AA composition, with reference to methods)
Plotting Tools - GIF Images, Postscript Images

Similarity Plot for aligned amino acid sequences, using 250 PAM
Hydropathy Plot for amino acid sequences

Viewing and Displaying X-ray and NMR Structures (links to manuals provided by Gail I. Schuman, Brookhaven National Lab, Biology Department, schuman@bnlstb.bio.bnl.gov)

Using RasMol

Using Kinmage

Users Manual
PreKin Utility (converts PDB format to KIN format)
Brief Exercises

Quantitative Analysis of DNAse1 Footprint Data - a detailed description of theory, methodology and computer analysis as applied to the Rhizobium meliloti DctD / dctA UAS system. This material complements articles by the Ackers' lab in their studies of the lambda repressor, providing a software solution for researchers using PC computers rather than a Unix or VAX mainframe system.
Webb Miller's Globin Server