CRPC-TR99810-S						August 1999

Title: Gene Trees: Phylogenetic Trees from Amino Acid Sequences

Author: Beckie Chan

Submitted November 1999

The goal of this program is to classify genes into families based on their
nucleotide and amino acid sequences.  From one gene, the program will find
related genes, sort them into subfamilies, families, and super families,
and organize them into phylogenetic trees.  Svjetlana Miocinovic, an
undergraduate at the California Institute of Technology, and I worked with
biologist from the University of California, Irvine, Dr. George A. Gutman
and Dr. K. George Chandy.  To maximize efficiency, this program has been
broken up into two parts.  Svjetlana used similarity search programs to
find related genes given one gene sequence.  My part involved taking these
related gene sequences to create a phylogenetic tree.  The whole Program
has been written in Java, so it can easily be made web accessible in the
future.  Once this website has been created, biologist, doctors and many
others can take advantage of it.

The current process used to generate sequence alignments and trees can be
extremely long and tedious.  One begins by obtaining sequence files from a
genetic sequence database (e.g. NCBI's GenBank [14].  Then, coding region
nucleotide sequence files and amino acid sequence files are created.  
These sequences are then formatted into another file for alignment.  Once
the sequences are aligned, the output is converted into a NEXUS format.  
This NEXUS file must be manually edited to include only the regions where
significant alignment exists among the sequences.  Finally, after this has
been done, a phylogenetic tree program is used to create the tree.

To make this process less laborious, a Java application is now available
to go directly from the given sequences to the phylogenetic tree, without
the need for manual tasks.  The program is composed of four classes:
Alignment, GroupMatch, MakeTree, and MainTree.  This document explains the
process of going from amino acid sequence to phylogenetic tree.

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Beckie Chan
pchan543@cs.caltech.edu
Department of Computer Science
California Institute of Technology