Lab 2 genomics natalia

The assessment is structured to take 1 hour and 15 minutes but students will receive 1 hour and 30 minutes to complete it.
Learning agreements will be noted; however, it is critical to submit them before the time elapses; failure to do so results in a score of zero.
- Emphasis on personal accountability: "It's your problem" if submission issues arise.

1 hour 15 minutes allocated for the assessment itself.
An additional 15 minutes is provided for saving the file, reviewing answers, and submission.
Student responsibility emphasized to avoid relying solely on notes during the assessment.

Notes may serve as a refresher but should not replace understanding of workflows.
Students cautioned: Reliance on notes risks potentially completing only 50% of the assessment.
Instruction: Notes should be basic guidelines, not full workflows.

No retakes will be offered for poor performance under current module conditions, unlike previous years where reviews were available.
Absences may be accommodated with proper certified documentation, and resets will be available during the week of December 1.
Important notice: Instructor will be on maternity leave the following week after assessments, advising students to manage their schedules.

Students may submit incomplete assessments if they run out of time as long as they submit before the end time; points will be given for what is completed.
Understanding that different questions carry different marks and importance emphasized.

An introduction to the use of the BLAST software for aligning query sequences with reference sequences was made.
Reminder that the importance of learning the rationale behind the BLAST tool will support their practical applications, including examples from gene therapy development.
- Emphasis on the need for alignment in biological research and genetic material integrity.

There are different types of BLAST: nucleotide BLAST and protein BLAST. Each has specific functions:
- Nucleotide BLAST: Compares a given nucleotide sequence (genomic or cDNA) against a database.
- Protein BLAST: Functions similarly, but compares amino acid sequences, using the language of amino acids.
Comparative approaches will be discussed regarding the software and the databases available through the NCBI platform.

The instructor details various RNA forms used in database searches, such as genomic DNA and cDNA, focusing on the significance of their differences in research.
- Students are encouraged to familiarize themselves with cDNA entries in their assessments.

The tutorial will involve navigating back to specific gene entries on the NCBI website, entering specific gene sequences, and how to select relevant database settings for proper querying.
Instructors will guide on how to select small base pair sequences for efficient searching, indicating that large genomic entries could be impractical for BLAST searches.

After conducting a BLAST search, results will reflect the similarity and scoring of matches:
- Score Mechanics: Every match scores points, mismatches deduct points, while gaps score neutral points.
- Scoring systems considered: how query coverage, percentage identity, and e-values correlate with the assessment of a good hit.
E-values analyzed in the context of statistical significance in bioinformatics, with emphasis that a good scientific result must meet more stringent thresholds than common laboratory expectations:
- Bioinformatics uses stricter e-value thresholds; e.g., a probability near zero signifies strong confidence in matches.

As the session transitions to protein-based analysis, the instructor introduces the concept of conserved sequences versus mutated sequences, stressing their importance in protein functionality.
Consequences of point mutations at both DNA and amino acid levels highlighted to illustrate the significance of structural changes, and discuss disulfide bonds in the context of key protein functions.

Conserved sequences are crucial in understanding the functionality across species. For instance, the similarity in antibody function across species is conveyed as an important area of study in biopharma therapeutics.

Students learn how inputs in BLAST can aid in experimental setups and hypothesis testing, with highlighted real-world contexts to use such as in plasmid verification.
Recommendations made for careful examination of e-values and sequence identities to ascertain valid research conclusions.

Students are warned to refrain from relying solely on theoretical understanding; practical application through real biology and in-use examples is vital for mastery of the content learned.