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    Initial Analysis:

    • Blasted the sequence against all genomes to find the best hits and to determine what organism our sequence was from
    • Used a dotplot to find potential repeats.
    • CpG Island search and Compseq to determine regions of high GC content. 
    • Repeatmaster to get the masked sequence.


    Gene Prediction:

    • GeneMark and FGENESH were run with both the masked and unmasked sequences to determine potential genes.
    • These genes were then compared with each other to see what gene predictions from the unmasked matched the masked prediction and also what predictions found in GeneMark matched predictions found using FGENESH.
    • all of the potential genes were than blasted using blastp and the blast hits were compared to one another.
    • After removing the hits that were retrotransposons, the remaining hits were blasted against the EST database to confirm that they are real genes. 


    Candidate genes:

    • Genes that were found to have ESTs were consiered to be out candidate genes, in which we found 2. 
    • The genome browser in phytozome was use to see if both genes existed and that all of them were found.
    • These two genes were than run with Blast2Go to get an idea of the functions with these genes. 
    • We then used I-Tasser to find the protein structure
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