Determining An Unknown Genomic Sequence of Arhodomonas sp. Seminole Through Polymerase Chain Reaction

Abstract

Our central focus is to see if halo.Contig697rc with an alignment at the head joins
with halo.Contig478 with an alignment at the tail. From our initial analysis using
BLASTX, we showed possibility of the gap of the amino acid to be filled. We used
BLASTX in order to determine the alignment of the given fused contigs and the
related protein. Primer Quest allowed us to use the fused contig in order to develop
forward and reverse primers to be used in PCR. The gel showed that further testing
needed to be done due to no definite sequence being found. We used BLASTX of the
genomic DNA flanking region by using the fused contig sequence in order to
determine a reference protein. No domains were detected. Dr. Canaan ran our PCR a
second time, and we were able to utilize ClustalW2 for multiple sequencing
alignments to find our final alignment results. Results were limited to the forward
primer, so further testing is required.