Human Alu Sequence Identification On-Line

Aleksandar Milosavljevic milosav at SPICA.UCSC.EDU
Fri Oct 19 19:33:29 EST 1990


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 cis.ucsc.edu.  For
questions and suggestions, contact pythia-admin at cis.ucsc.edu.

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

APPENDIX: The help message from pythia at cis.ucsc.edu .

Pythia first aligns the incoming sequence (your message must contain
only one sequence) against the Alu consensus and then checks the
sequence for the bases that are diagnostic for Alu subfamilies J, Sb,
Sc, Sp, Sq, and Sx.  The Alu consensus and the diagnostic positions
are described by J. Jurka and A. Milosavljevic in "Reconstruction and
Analysis of Human Alu Genes", J. Mol. Evol. (to appear).

The sequence should be sent in Intelligenetics format, which means
that it should terminate with '1' and should be preceeded by a name on
a line by itself. The name should be unique, but it should start with
'ALU'.  An example follows.


For further questions and suggestions contact pythia-admin at cis.ucsc.edu .

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