This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Giardia lamblia is a waterborne parasitic protist that colonizes the intestinal tracks of mammals. It is also one of the first organisms to diverge from the primary evolution pathway of eukaryotes, and as such may provide insight into the biochemical makeup of early eukaryotes. UTEP is one of the collaborating institutions in the shotgun sequencing of the giardial genome, headed by Mitchel Sogin at the Marine Biology Laboratories at Woods Hole, MA. The shotgun sequencing coverage now exceeds 11x. This data is currently assembled using the ARACHNE assembler, and that is the version which will be published. This assembly, however, has critical problems associated with a gene family, the Variant Specific Proteins (VSPs). In particular, many of the existing breaks in the assembly are associated with occurrences of pairs of these genes. We propose to take the raw sequence files and to reassemble them using the EULER assembler, using Eulerian path approach, and to compare the resulting assembly with the ARACHNE assembly, particularly in the areas of VSP genes.
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