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Sequence Analysis Tools

I've written a couple of simple web based tools for sequence manipulation. These programs were developed in-house, if you would like any others, or have any suggestions, please pass them on to humberto -at- hpcf.upr.edu, carlos -at- hpcf.upr.edu, or submit it to our HelpDesk help -at- hpcf.upr.edu.

Multiple Sequence Alignment

Click here to align nucleotide or amino acid sequences. This is a simple interface to Clustal W 1.7. Output is the output of clustalw followed by the .aln file. If you need nicer output, try loading the .aln file into the BOXSHADE server, or another alignment pretty printer. The GeneDoc program is absolutely the best multiple sequence alignment display and editing tool I have ever seen.

Sequence Assembly

Click here to run CAP, the contig assembly program. This program takes multiple reads from the same sequence, in either forward or reverse direction, and tries to assemble them into a single contig. This version of CAP outputs a fasta format file, suitable for entering into a multiple sequence alignment display program.

Transmembrane Structures

The memsat program is described in it's documentation file as:

implements a new method for the prediction of the secondary structure and topology of all-helix integral membrane proteins based on the recognition of topological models. The method employs a set of statistical tables (log likelihoods) compiled from well-characterized membrane protein data, and a novel dynamic programming algorithm to recognize membrane topology models by expectation maximization. The statistical tables show definite biases towards certain amino acid species on the inside, middle and outside of a cellular membrane.

The method is described in the following reference:

"Jones, D.T., Taylor, W.R. and Thornton, J. M. (1994) Biochemistry. 33:3038-3049."

Commercial use of memsat requires a license from the author, please see the memsat home page

Custom Blast

Carlos Rodriguez (carlos -at- hpcf.upr.edu) and I implemented a cobbled together custom blast and parser for Dr. Owen McMillan's Functional Programming class. It's temporarilly available here, but Carlos and I will be putting it up on a production server soon. We're also working on pepinoblast, a blast that finds large new open reading frames, for Dr JE Garcia's lab.

Most recent change: 2007/9/3 at 22:21
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