02/06/19

Rationale:

to learn to completely annotate a gene.

Procedure:

1. opened  DNA master
2. Opened FastA file for elesar using the following steps, File>open>FastA multiple sequence file> Choose Elesar.FastA
3. clicked export on window with the extracted file and then choose Create sequence from this entry only.
4.  to see the frames, went to DNA> Frames.
5. then clicked ORF on the new window to see the highlighted genes.
6. Opened phage notes and enter data as directed by the spreadsheet.
7. Used starterator after blasting the gene in phagesdb. done to acquire information to be entered in the spreadsheet
8. Learned to use phamerator.

Results:

Gene 14

SSC:8837 – 9250, CP:No no start codon avaiable to cover the coding potential , SCS:Both, ST:SS, BLAST-Start:Aligns with Arhtrobacter sp. ok362 gpn/a NCBI BLAST q14:s1 0.97 0, Aligns with phage Ryan gp14 PhagesDB BLAST q14:s2 0.78 3E-46, Gap:4bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 2.751 -3.809 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Gene 15

SSC: – , CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter sp. Hiyo 6 gpn/a NCBI BLAST q15:s1 0.97 4E-97, Aligns with Arv2 gp11 PhagesDB BLAST q15:s2 0.78 4E-78, Gap:56bp gap, LO:Yes, RBS:Kibbler7 and Karlin Medium 2.801 -3.226 No, F:NKF, SIF-BLAST: Supported by PhagesDB BLAST gp , , SIF-HHPred:NKF, SIF-Syn:NKF

Conclusion:

Phage notes is better for entering data than DNA Master. Now, we have all the tools we need for annotation.

Future Steps

get ready to annotate Napoleon B