Human Alu Identification On-Line

Aleksandar Milosavljevic milosav at SPICA.UCSC.EDU
Fri Oct 19 18:43:23 EST 1990

The following is an abstract that (by mistake) did not appear
in the Proceedings of the Biomatrix 90 Workshop. I hope at least
some of you will find it useful. -Aleksandar Milosavljevic


by Aleksandar Milosavljevic and Jerzy Jurka, 
Linus Pauling Institute of Science and Medicine,
and Pat Monardo, 
Cold Spring Harbor Laboratories

The identification program is based on our current paper (J.Jurka and
A.Milosavljevic, Reconstruction and Analysis of Human Alu Genes, J.
Mol. Evol., to appear) where we propose that Alu sequences are mostly
pseudogenes retroposed from a set of biologically active Alu genes.
Severel subfamilies of Alu sequences, named J, Sb, Sc, Sx, Sp, and Sq,
have been retroposed from particular genes, or closely related sets of
genes.  In its present form, the program reads the incoming electronic
mail message that contains an Alu sequence, aligns it against the Alu
consensus and then examines the diagnostic positions for the presence
of bases characteristic for the particular Alu subfamilies.  A short
output file containing the results is then mailed back to the sender.
To obtain detailed information about the input format and the current
status of our program, please send a message containing the single
word "help" to the Internet address pythia at  For
questions and suggestions, contact pythia-admin at

We gratefully acknowledge Prof. David Haussler from the Baskin Center
for Computer and Information Sciences, UC Santa Cruz for his support
of this project.

More information about the Biomatrx mailing list