DNA identification, sequencing, BLAST, controls, query coverage, and E-value.
What to do if absent- CER:
- Claim, Evidence, Reasoning — make a claim, back it with evidence, explain your reasoning.
- SOP:
- Standard Operating Procedure — the exact steps to follow (especially in a lab).
- Tracker:
- Your PLTW progress log where you record completed evidence.
- myPLTW:
- The PLTW course site where you do the online activities — you open it through Schoology.
Week overview - Who is the culprit? Identifying a pathogen with DNA and BLAST
Use a DNA sequence and BLAST to identify an unknown bacterial pathogen and judge match quality with E-value and query coverage.
- 1Open the case file and copy the unknown DNA sequence into a scratch doc so you do not lose it.
- 2Go to NCBI BLAST, choose nucleotide BLAST, and paste your unknown sequence into the query box.
- 3Run the search, then sort the hit table and read the top match name, percent identity, and E-value.
- 4Record the query coverage and E-value for your top hit; note that a smaller E-value means a stronger match.
- 5Compare your top hit to a control sequence the teacher provides to confirm the workflow is behaving.
- 6Write one sentence naming the likely pathogen and the evidence (top hit, E-value, query coverage) that supports it.
- • You will be able to run a nucleotide BLAST search and read the hit table.
- • You will be able to explain what E-value and query coverage tell you about a match.
- • You will be able to name an unknown pathogen and back it with sequence evidence.
Daily lessons this week
Open any day for its full lesson, the work due that day, and guided notes.
Notebook entry: four DNA bases with pairing rules, two-sentence sequencing summary, and one question for the BLAST lab.
BLAST hit table screenshot with top organism name and percent identity annotated; one-sentence identification statement; control run result.
Two-hit comparison table (E-value, query coverage, percent identity) and revised identification statement citing all three metrics.
Pathogen-ID report: claim naming organism, reasoning paragraph citing E-value/query coverage/percent identity, control validation explanation, and one limitation sentence.
Quick intro to the week
- Hook: a real outbreak gets solved when investigators read DNA the way you are about to.
- Today's goal: turn an unknown sequence into a named pathogen using BLAST and defend your call.
- Monday's bioethics debate on data sharing connects here: open sequence databases are why BLAST works at all.
- Reminder: your graded BLAST screenshots and write-up live in the PLTW course shell, not on paper.
Your PLTW coursework this week
Do this: Advance the PLTW Unit 1 pathogen-identification benchmark in the online course shell after today's BLAST run.
- • DNA sequences can act as a fingerprint that identifies an organism.
- • BLAST compares a query sequence against a database of known sequences.
- • Interpret E-value and query coverage to rank BLAST matches.
- • Use a control sequence to check that a sequencing workflow is reliable.
📋 PLTW tracker evidence due this week: BLAST hit screenshot plus a written pathogen identification with E-value and query coverage.
All PLTW activities are completed inside the PLTW course environment — this page only gives direction.
This week's PLTW tracker
Your week at a glance. Check off each deliverable as you finish it, then submit so Mr. Mendoza can see how the class is pacing.
Use the code Mr. Mendoza gave you, not your name. Saved on this device.
| Day | Date | Focus | Key deliverable |
|---|---|---|---|
| Tuesday | Mon, Feb 1 | DNA sequencing basics | Notebook entry: four DNA bases with pairing rules, two-sentence sequencing summary, and one question for the BLAST lab. |
| Wednesday | Tue, Feb 2 | BLAST computer lab | BLAST hit table screenshot with top organism name and percent identity annotated; one-sentence identification statement; control run result. |
| Thursday | Wed, Feb 3 | E-value and query coverage | Two-hit comparison table (E-value, query coverage, percent identity) and revised identification statement citing all three metrics. |
| Friday | Thu, Feb 4 | Pathogen-ID report submission | Pathogen-ID report: claim naming organism, reasoning paragraph citing E-value/query coverage/percent identity, control validation explanation, and one limitation sentence. |
- M: no school
- T: debate post + BLAST intro
- W: shortened-day sequence check
- Th: BLAST interpretation
- F: pathogen ID ticket
Due by week's end: Pathogen ID mini-report.
Lab day — what to bring & watch
This explainer accompanies the PLTW lab protocol — watch it before lab.
What to do when absent
Most days, this class is your PLTW coursework — and PLTW is online and individual. So being out usually just means doing exactly what we did in class, from home.
Open Schoology (CMSD) and keep goingHow to get there: open the CMSD website, click Clever, sign in with your Microsoft (district) account, then open Schoology from Clever.
You can't do those from home — do this instead: Virtual bacterial ID with screenshot explanation.
Class still runs. A substitute will post today's plan — complete the online activity above; it's built to be self-guided. Need the concept taught without a teacher? Use this authoritative explainer:
NCBI BLASTVocabulary
Virtual resources
Teacher-posted resources
Classroom documents for this lesson. Ones marked “Open the file” open right here; the rest are posted in Schoology. Use the label on each card to choose the right move.
Open this when the class reaches this activity and use it to complete the required lesson artifact.
Placement rationale
Matched Pathogen identification, PCR, sequencing, BLAST by path:Medical-Interventions/Unit-1_How-to-Fight-Infection/1.1_The-Mystery-Infection; keywords:blast, sequencing, pathogen, dna, identification. Score 162. Visibility: student-schoology (student-facing resource; link through Schoology rather than local path).
Use this after the required lesson work when you are ready for a harder application or a deeper connection.
Placement rationale
Matched Pathogen identification, PCR, sequencing, BLAST by path:Medical-Interventions/Unit-1_How-to-Fight-Infection/00_Unit-Overview; keywords:blast, pathogen, dna, identification. Score 150. Visibility: student-schoology (student-facing resource; link through Schoology rather than local path).
Use this if you were absent, got stuck, or need another pass before you submit the lesson artifact.
Placement rationale
Matched Pathogen identification, PCR, sequencing, BLAST by path:Medical-Interventions/Unit-1_How-to-Fight-Infection/00_Unit-Overview; keywords:blast, pcr, pathogen, identification. Score 150. Visibility: student-schoology (student-facing resource; link through Schoology rather than local path).
How to get there: open the CMSD website, click Clever, sign in with your Microsoft (district) account, then open Schoology from Clever.
Standards this week
WebXam practice
Drop your Week 3 here. Use a clear file name (your initials + project). Routine work still goes to Schoology (via the CMSD portal).
Upload a project