DNA identification, sequencing, BLAST, controls, query coverage, and E-value.
Your PLTW coursework: Medical Interventions ▸ Unit 1: How to Fight Infection ▸ Lesson 1.1 The Mystery Infection ▸ "Activity 1.1.3 Using DNA to Identify Pathogens"
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. Find it in Clever with your Microsoft sign-in, right next to Schoology.
Week overview - Who is the culprit? Identifying a pathogen with DNA and BLAST
Use a and to identify an unknown bacterial and judge match quality with E-value and .
- 1Open the case file and copy the unknown into a scratch doc so you do not lose it.
- 2Go to NCBI , 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, , and E-value.
- 4Record the 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 is behaving.
- 6Write one sentence naming the likely and the evidence (top hit, E-value, ) that supports it.
- • You will be able to run a nucleotide search and read the hit table.
- • You will be able to explain what E-value and tell you about a match.
- • You will be able to name an unknown 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 lab.
hit table screenshot with top organism name and annotated; one-sentence identification statement; control run result.
Two-hit comparison table (E-value, , ) and revised identification statement citing all three metrics.
-ID report: claim naming organism, reasoning paragraph citing E-value//, 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 using and defend your call.
- Monday's bioethics debate on data sharing connects here: open sequence databases are why works at all.
- Reminder: your graded 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 -identification benchmark in the online course shell after today's run.
- • DNA sequences can act as a fingerprint that identifies an organism.
- • compares a query sequence against a database of known sequences.
- • Interpret E-value and to rank matches.
- • Use a control sequence to check that a sequencing is reliable.
📋 PLTW tracker evidence due this week: hit screenshot plus a written identification with E-value and .
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 |
|---|---|---|---|
| Thursday | Thu, Sep 10 | DNA sequencing basics | Notebook entry: four DNA bases with pairing rules, two-sentence sequencing summary, and one question for the BLAST lab. |
| Friday | Fri, Sep 11 | BLAST computer lab | BLAST hit table screenshot with top organism name and percent identity annotated; one-sentence identification statement; control run result. |
| Monday | Mon, Sep 14 | E-value and query coverage | Two-hit comparison table (E-value, query coverage, percent identity) and revised identification statement citing all three metrics. |
| Friday | - | 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.
4 panels from the illustrated semester.
Fiction. There is no such student. The lessons, labs and dates are the real planned course; the student, the classmates and the conversations are invented.
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 Clever, then myPLTWHow to get there: open Clever and sign in with your Microsoft (district) account. Both myPLTW and Schoology are in Clever. Do the activity in myPLTW. Turn the work in on this site or hand it to Mr. Mendoza, because that is the step that counts as submitted. Schoology only shows your report-card grade later.
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 are posted in Schoology. Open Clever, then Schoology, and find each one by the name shown on its card.
Open this when the class reaches this activity and use it to complete the required lesson artifact.
Placement rationale
Matched identification, PCR, sequencing, 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 identification, PCR, sequencing, 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 identification, PCR, sequencing, 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 Clever and sign in with your Microsoft (district) account. Both myPLTW and Schoology are in Clever. Do the activity in myPLTW. Turn the work in on this site or hand it to Mr. Mendoza, because that is the step that counts as submitted. Schoology only shows your report-card grade later.