September
5
Lab 2: Gene Annotation
Title: Gene Annotation
Date: 9/5/17
Objective:
Our purpose is to learn how to prepare for auto-annotate on BLAST and Gene Mark.
Procedure:
- download Link.fasta file from phages DB and add it to DNA Master
- Go to https://discover.kbrinsgd.org/autoannotate/
- select and copy the entire content on to Pecaan
- Set Translation to Bacteria and Plant Plastid Code
- For BLAST, click on gene 2
- click DNA, ORFS
- click on start codon and click RBS
- Go to DNA Master (product) and copy it to BLAST
- For Gene Mark, Go to Gene Mark link on canvas
- upload the Link.fasta file
- use PDF and receive a document for the Gene Mark reading
- For annotating in DNA Master, and type in notes
Results:
SSC: GAP:216 CP: SD: Z:-4.441 SCS: NCBI Blast: PDB BLAST:
HHPred:Agree E value: 4e-43 LO: Agree ST: F: FS:
Start Codon: 345
Conclusion:
The Link phage undergone many testings in bacteriophage databases such as Gene Mark and BLAST and both agreed to have the same name. Each database specializes in different functions. BLAST compares new sequences with sequences of known or assumed function. Gene Mark illustrated the gene strands to see if the gene was covered by the data analysis.
Future Plans:
I hope to be able to have my DNA Master to work on my own laptop so that I can easily store my information. Also, I hope to become familiar with all of the databases.