Hey guys! I really think that everyone should take time to read this!
http://www.jyi.org/issue/identification-of-dna-sequences-of-long-terminal-repeat-retrotransposons-in-maize/
During September of 2005 Joseph L. Wezenter analyzed maize sequences at Montclair University. The goals of his project were similar to that of Phoenix’s group project- to determine what Long Terminal Repeats retrotransposons and what genes are present in maize (for us Amigo), to find the start and stop locations of both, and to ultimately create physical maps depicting their locations.
With the raw sequence from the FASTA file, a web-based piece of software called GenScan was used. GenScan predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms such as maize. By being organismspecific, the results are more precise. The FASTA sequences were loaded and maize was selected as the organism. From this the one letter amino acid sequences of the predicted genes were generated and uploaded into BLASTp (protein-protein) of the NCBI website for further analysis.
TIGR (http://www.tigr.org/tdb/e2k1/plant.repeats/) is another piece of web-based software Joseph used. It is a collection of curate databases containing DNA and protein sequences, gene expression, cellular role, protein family, and taxonomy of microbes, plants, and humans (TIGR 2005).
A phylogenetic analysis was also preformed on these LTRs. It was depicted in a TreeView diagram that represented a pedigree of inherited relationships among molecules, organisms, or both. (Like I know one of the other groups did!!)