WICGR Develops New Assembly Program

The computer program, called Arachne 2, can produce a high quality sequence and do so with a great deal of accuracy and little computational power.

Arachne 2 assembled the complete genome sequence of the mouse in only 14 days and required only a single Compaq Alpha processor running at 833 MHz. It could do so with less than 32-Gb RAM, one quarter of what its predecessor would have needed. The predecessor, Arachne 1, was able to assemble genomes of intermediate size-genomes of flies, worms, and pufferfish, for instance-and was used to assemble the sequence of the fungus Neurospora crassa.

l. to r. - Sante Gnerre, Evan Mauceli, Eric Yee, Jonathan Butler, David B. Jaffe, Jade Vinson.

Arachne 2 takes whole genome assembly to the next level. It is able to assemble larger, mammalian-size genomes at a much higher quality.

Because Arachne 2 assembles genomes in larger pieces than the previous version, it enables biologists to know more of the exact sequence on the region being studied. It also reduces the number of gaps within supercontigs -or long strings of sequence -which increases the chances that regions of interest will be in one piece.

The Arachne 2 assembly algorithms are described in the January issue of the journal Genome Research.

"Publicly available genome sequence assemblers like Arachne 2 will make it possible to sequence the genomes of other species accurately and efficiently. This is an important next step because this knowledge will help researchers unravel the mysteries of the human genome, " says David Jaffe, a researcher at the Genome Center who is lead author on the paper.

Scientists have also used Arachne 2 to assemble bacterial genomes of the species Mesoplasma and Mycoplasma, and other genomes Magnaporthe, Ciona, and Tetraodon.

Sequencing of the genomes of other species is an important next step of the Human Genome Project because the knowledge will help researchers unravel the mysteries of the human genome. Comparing the human genome to those of other species helps researchers identify important genetic elements conserved through evolution.

The current version of the ARACHNE 2 will be freely available this month as both source code and executable for Compaq Alpha machines (http://www-genome.wi.mit.edu/wga).

The title of the paper is "Whole Genome Sequence Assembly for Mammalian Genomes: Arachne 2" and the authors are David B. Jaffe, Jonathan Butler, Sante Gnerre, Evan Mauceli, Kerstin Lindblad-Toh, Jill P. Mesirov, Michael C. Zody and Eric S. Lander.

For more information, contact:
Seema Kumar, 617.252.1420