milosav@SPICA.UCSC.EDU (Aleksandar Milosavljevic) (10/20/90)
HUMAN ALU SEQUENCE IDENTIFICATION VIA ELECTRONIC MAIL 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@cis.ucsc.edu. For questions and suggestions, contact pythia-admin@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@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. ALU007 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGG TCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCG GGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTC TCAAAAAAAA1 For further questions and suggestions contact pythia-admin@cis.ucsc.edu .