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.
Commercial use of memsat requires a license from the author, please
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.
Humberto Ortiz Zuazaga
Most recent change: 2007/9/3 at 22:21
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