1/30/19

Rational:

To continue annotation and learning how annotate gene 1. Annotated what has been learned thus far for gene 20 and 21.

Procedure:

• Opend the auto-annotated Elesar
• Calculated the gap/overlap between the upstream gene from gene 1
• Determined whether the gene was the longest ORF
• Selected the gene and pressed the RBS button to get the Z-score, final score and determine whether the current ORF is the best according to the RBS
• For gene 20 and 21 found the SSC
• Looked at GeneMark to determine if the gene covers the coding potential
• Found the longest ORF
• BLASTed the proteins for gene 20 and 21
• Wrote down the name of the phage name that aligned with the gene and the gene number
• Wrote what database the alignment was found in
• Determined what basepair the query and the subject started matching at
• Found the e-value for the match (shows the likelihood the alignment was random)

Observations:

• Gene 1 is the first gene so in gap 1st gene was written
• The gene was pushed back to an earlier start making it the longest ORF
• Entered the scoring and spacing matrix under the RBS (Kibler7 and Karlin Medium)
• The Z-score was not the best for the current start, but it was determined that it was still the best
• Both alignments for gene 20 and 21 were from NBCI

Conclusion:

The annotations up to RBS were finished for gene 1. Genes 20 and 21 were then also annotated up to the same point. Next lab I will finish learning how to do the rest of the annotations steps and practice on gene 20 and 21.