BLAST (1/28/19)
Rationale: Go over guiding principles along with other analysis tools, such as GeneMark and BLAST and start to fill in the notes template.
Tools:
- DNA Master
- NCBI
- PhagesDB
- GeneMark
Procedure:
- In DNA Master, the main window, the frames window, and the choose ORF start window were opened.
- BLAST was performed on Elesar gene 1 using both NCBI and PhagesDB.
- The SSC, CP, and SCS portions of the template for Elesar gene 1 were filled out.
- This annotation was saved.
Results:
After performing BLAST through both NCBI and PhagesDB, it was determined from the high E value that there was no significant alignment found. The images below show these results.
It was determined through GeneMark that the start choice (84 bp) predicted by Glimmer and GeneMark was not the LORF (longest open reading frame). At 45 bp, all possible coding potential was covered as shown in the GeneMark graph below.
The following screenshot shows what parts of the template where filled in along with the values in the choose ORF start window.
Conclusion:
Although it is rare to see TTG as a start codon, it can be a start codon. The start choice predicts from Glimmer and GeneMark are not always accurate.
Future Work:
The result of Elesar gene 1 template will be filled out.
