BLAST computer lab
Safety gate · before any work
- No biological materials in this session; standard computer lab rules apply.
- Do not close the BLAST results page before you screenshot it. Use Cmd+Shift+4 (Mac) or the Snipping Tool (Windows) to capture.
- Save your screenshot to your portfolio folder right away, not just to the desktop.
Do now
Use nucleotide BLAST to compare an unknown DNA sequence against a database and read the hit table.
- Hand in
- BLAST hit table screenshot with top organism name and percent identity annotated; one-sentence identification statement; control run result.
- Where
- Turn this in at the drop folder with your district Microsoft sign-in, or hand it to Mr. Mendoza in class. Both count as submitted. Doing the activity in myPLTW does not.
You get two school days for every day you were absent, so this deadline moves with you.
You have a real unknown DNA read from the case file. When you paste it into and hit search, what does the top hit's organism name and actually tell you about your patient's ?
Use nucleotide to compare an unknown against a database and read the hit table.
- • You will be able to run a nucleotide search.
- • You will be able to read an organism name and from a hit table.
- • You will be able to use a control to check your .
- Before you touch the computer, write what you think is comparing your sequence against.
- Why might a scientist run a KNOWN sequence through the tool first, before trusting it on an unknown?
- 1Copy the unknown from the case file into a scratch document so you do not lose it.
- 2Go to NCBI , choose nucleotide BLAST, and paste your sequence into the query box.
- 3Run the search, then read the top hit's organism name and .
- 4Take a screenshot of the hit table for your portfolio.
- 5Run a control sequence the teacher provides to confirm the behaves.
- 6Write one sentence naming the likely organism and the evidence behind it.
What did this day actually feel like?
BLAST computer lab
LAB The whole class in the computer lab running BLAST, which compares an unknown sequence against a global database and ranks what it matches.
Watching an unknown resolve into a named organism in about forty seconds is the first time this course felt like the actual job. The database is public. Anyone can do this.
Turned in: lab report → Lab Reports folder
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.
The same day, drawn.
The whole class in the computer lab running BLAST, which compares an unknown sequence against a global database and ranks what it matches.
ME
A confident top hit that covers a tenth of your sequence means nothing. I would have been fooled yesterday.
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.
🛠 Get unstuck · pick your level
Lab day: Tier 1 is the whole class at the bench. No extension today.
🔑 Today's words · 5
Tap a word in the lesson for a plain meaning and one example. Recycled into next week's Do-Now.
Do the work · 80-minute blockfirst 5 min = hook▸
💡 Big idea: aligns your unknown read against millions of known sequences and ranks the matches, so a strong top hit names the organism, but only a passing control run proves the answer can be believed.
- 0-8 minOpen NCBI ; review the interface and identify the query box, database selector, and results area
- 8-20 minCopy unknown sequence from case file into a scratch doc; paste into query box and run search
- 20-35 minRead the hit table: find top organism name and ; screenshot and save to portfolio folder
- 35-50 minRun the teacher-provided control sequence; compare results to expected organism to validate
- 50-65 minWrite one sentence naming the likely organism and citing the as evidence
- 65-80 minShare results with a partner; compare top hits and discuss any discrepancies
- • NCBI is a free public tool used by researchers worldwide; learning it today gives you a skill you can use in any biology career.
- • The same database you'll search holds sequences from every outbreak ever identified.
- • Work carefully and save your results immediately; a lost screenshot means starting over.
- • Exit goal: a screenshot of your hit table and one sentence naming the likely organism.
- • (Basic Local Search Tool) aligns a query sequence against millions of known sequences and returns the closest matches.
- • The hit table shows organism name, , and E-value; the top hit with the highest identity and lowest E-value is the best match.
- • Running a known control sequence confirms the tool and your are working correctly before trusting an unknown result.
DNA identification, sequencing, BLAST, controls, query coverage, and E-value. · computer lab
Day 2 of this lesson. Open this exact section in myPLTW (find it in Clever, Microsoft sign-in), then do the work below.
Do this: Open Activity 1.1.3 Using DNA to Identify Pathogens in myPLTW and retrieve the unknown sequence from the case file for the computer lab.
Run both the unknown and control sequences in ; screenshot the hit table.
Sequencing summary and question should be done (Tuesday); hit table screenshot due today.
Hit table screenshot in portfolio folder and identification sentence in notebook.
The official PLTW activity stays inside myPLTW. If myPLTW will not open, use F1 and E1-E3 on this page to complete today's local evidence decision, then make up the official activity when access returns. Turn this in at the drop folder with your district Microsoft sign-in, or hand it to Mr. Mendoza in class. Both count as submitted. Doing the activity in myPLTW does not.
Check things off as you work, then submit. This tells Mr. Mendoza how you're doing so he can help the class. It does not replace turning in your producible through the submission route shown below.
Use the code Mr. Mendoza gave you, not your name. Saved on this device.
DNA identification, sequencing, BLAST, controls, query coverage, and E-value. · BLAST computer lab
Open Activity 1.1.3 Using DNA to Identify Pathogens in myPLTW and retrieve the unknown sequence from the case file for the computer lab.
Sequencing summary and question should be done (Tuesday); hit table screenshot due today.
This is how Mr. Mendoza sees the class keeping pace with PLTW. Be honest, it only helps if it is accurate.
🎯 Use nucleotide to compare an unknown against a database and read the hit table.
- Copy the unknown from the case file into a scratch document so you do not lose it.
- Go to NCBI , choose nucleotide BLAST, and paste your sequence into the query box.
- Run the search, then read the top hit's organism name and .
- Take a screenshot of the hit table for your portfolio.
- Run a control sequence the teacher provides to confirm the behaves.
- Write one sentence naming the likely organism and the evidence behind it.
Lab report: hit table screenshot with top organism name and annotated; one-sentence identification statement; control run result.
Turn this in at the drop folder with your district Microsoft sign-in, or hand it to Mr. Mendoza in class. Both count as submitted. Doing the activity in myPLTW does not. Use the checklist just below and upload by 11:29 PM for full credit. Absent with an excused absence? You get two school days for every day you were absent, so this deadline moves with you.
| Task | Who |
|---|---|
| Copy the unknown from the case file into a scratch document so you do not lose it. | _______ |
| Go to NCBI , choose nucleotide BLAST, and paste your sequence into the query box. | _______ |
| Run the search, then read the top hit's organism name and . | _______ |
| Take a screenshot of the hit table for your portfolio. | _______ |
| Run a control sequence the teacher provides to confirm the behaves. | _______ |
| Write one sentence naming the likely organism and the evidence behind it. | _______ |
Working solo? Put your own name in "Who" for every row.
- You will be able to run a nucleotide search.
- You will be able to read an organism name and from a hit table.
- You will be able to use a control to check your .
- 1Do thisUse nucleotide BLAST to compare an unknown DNA sequence against a database and read the hit table.
- 2Use this resource
- 3Submit thisLab report: BLAST hit table screenshot with top organism name and percent identity annotated; one-sentence identification statement; control run result.
- 4Submit it here
- 1Open the drop folder.
- 2Sign in with your district Microsoft account, not a personal one.
- 3Upload the file, named Lastname_Firstname__Assignment Title.
- 4Your own upload panel says Uploaded with a green check: that is your receipt.
Turn this in at the drop folder with your district Microsoft sign-in, or hand it to Mr. Mendoza in class. Both count as submitted. Doing the activity in myPLTW does not. Genetics of Disease (Medical Interventions) › DNA identification, sequencing, BLAST, controls, query coverage, and E-value. › Lab reportOpen the drop folder
Learn it · deck, reading, and vocabulary▸
The deck carries the prior idea forward, lets you inspect an analogy, maps the rule to biology, and ends with the same evidence decision and exit ticket used on this page.
Generated from this lesson's canonical data with a red-team citation check.
A CER convinces a reader because its reasoning explains why each piece of evidence supports the claim, so drawing from multiple sources and linking them explicitly turns a week of clues into a defensible conclusion.
aligns your unknown read against millions of known sequences and ranks the matches, so a strong top hit names the organism, but only a passing control run proves the answer can be believed.
A library keeps a master plan protected while working copies guide production at different stations.
- Why protect the master copy?
- What information moves?
- Where can an error change the final product?
Stored information can be copied, read, and converted into a functional product.
Genes are regulated biological sequences, not conscious instructions, and one gene rarely determines a whole trait alone.
- • Master plan maps to DNA.
- • Working copy maps to RNA.
- • Production output maps to or a regulated cell function.
Driving question: You have a real unknown DNA read from the case file. When you paste it into and hit search, what does the top hit's organism name and actually tell you about your patient's ?
What you already know: A CER convinces a reader because its reasoning explains why each piece of evidence supports the claim, so drawing from multiple sources and linking them explicitly turns a week of clues into a defensible conclusion.
New idea: aligns your unknown read against millions of known sequences and ranks the matches, so a strong top hit names the organism, but only a passing control run proves the answer can be believed.
Visual or model: F1. F1. A lesson illustration or teaching diagram for BLAST computer lab. Use it with E1-E3; it is a model or context image, not experimental or patient data. What to notice: Trace the labeled testing, treatment, or biological process and identify where evidence limits the decision.
- Observe or measure the relevant feature in computer lab.
- Organize the observation with a stable evidence ID.
- Apply this rule: Stored information can be copied, read, and converted into a functional product.
- Choose the option the evidence supports and state the limit of the conclusion.
Real biomedical example: You have a real unknown DNA read from the case file. When you paste it into and hit search, what does the top hit's organism name and actually tell you about your patient's ?
What the evidence supports: E1-E3 and F1 support the daily take-home when the response meets the stated success criteria.
What it cannot prove: The package does not support claims beyond this lesson's or any real patient diagnosis.
- • : The exact order of the four bases (adenine, thymine, guanine, cytosine) along a strand of DNA, which spells out genetic instructions.
- • PCR: Polymerase chain reaction, a lab technique that uses heat cycles and an to make millions of copies of a chosen DNA segment.
- • : A DNA reading method that uses chain-terminating dideoxynucleotides to make fragments of every length, then sorts them by size to reveal the base order.
- • : A search tool (Basic Local Search Tool) that compares a DNA or sequence against a database to find similar sequences and likely relatives.
- • E-value: In a search, a number estimating how many matches that strong you would expect by chance alone, so a smaller E-value means a more meaningful hit.
- • : In a sequence search, the percentage of your input sequence that lines up with a database match, showing how much of it was compared.
- • control: The comparison condition that isolates the effect of the variable being tested by keeping everything else the same.
Use it now: Choose one decision option. Cite E1 and E3, then explain how the rule connects the evidence to your choice.
Go further, optional: The source links below are optional enrichment. Every fact required for today's local evidence decision appears in this lesson package.
(Basic Local Search Tool) aligns a query sequence against millions of known sequences and returns the closest matches.
Limit: E1 supplies context or an observation; it does not by itself establish the explanation.
aligns your unknown read against millions of known sequences and ranks the matches, so a strong top hit names the organism, but only a passing control run proves the answer can be believed.
Limit: E2 is a teaching statement or comparison and must be checked against the task evidence.
You will be able to run a nucleotide search.
Limit: E3 supports only the result or product criterion named here; it cannot justify a broader clinical or causal claim.
PLTW-GEND-2026-09-10 · Simulated classroom evidence scenario
Your role: medical interventions team member
Decision: Your team must decide what the evidence from computer lab supports before submitting the lab report named on the lesson page.
- • Proceed because the readiness evidence is complete.
- • Pause and correct the named setup or gap.
- • Repeat the measurement because quality controls are not acceptable.
Response: State one choice, cite at least two evidence IDs, explain the rule that connects them, and add one limitation. Submit it as the lab report.
Claim ceiling: The supplied lesson evidence can support an observation, pattern, classroom mechanism, or next-step decision about computer lab. It cannot by itself prove causation, establish a real clinical diagnosis, or justify action outside this classroom task.
Reason for review: Your team must decide what the evidence from computer lab supports before submitting the lab report named on the lesson page.
Context: Matching an unknown sequence against a database of known sequences turns raw letters into an identification, and running a known control first is what makes that identification trustworthy.
- • T1: Copy the unknown from the case file into a scratch document so you do not lose it.
- • T2: Go to NCBI , choose nucleotide BLAST, and paste your sequence into the query box.
- • T3: Run the search, then read the top hit's organism name and .
- • T4: Take a screenshot of the hit table for your portfolio.
- • T5: Run a control sequence the teacher provides to confirm the behaves.
- • T6: Write one sentence naming the likely organism and the evidence behind it.
- • E1: (Basic Local Search Tool) aligns a query sequence against millions of known sequences and returns the closest matches.
- • E2: aligns your unknown read against millions of known sequences and ranks the matches, so a strong top hit names the organism, but only a passing control run proves the answer can be believed.
- • E3: You will be able to run a nucleotide search.
Measurements: Use only the measurements, units, graph, or counts supplied in today's task. No additional patient measurement is implied.
Figure finding: Teaching diagram for computer lab. Trace the labeled testing, treatment, or biological process and identify where evidence limits the decision. This is a teaching model, not patient or experimental data.
Uncertainty: This is a composite classroom scenario. Missing history, measurements, or confirmation tests remain unknown and limit the conclusion.
Mean = sum of values / number of values. Median = middle ordered value. Range = maximum - minimum.
For 2, 4, 4, and 10: mean = 20 / 4 = 5, median = 4, and range = 10 - 2 = 8.
Mean, median, and range keep the measurement unit. Order the values before finding the median.
Calculate the requested summary for today's supplied values, then write what it reveals and what it hides.
- • The solution must address the stated need in computer lab.
- • The decision must be supported by E1-E3.
- • The final product must make the success criteria visible.
- • Complete the work inside the 80-minute block.
- • Use only supplied or teacher-approved materials and evidence.
- • Do not trade , accessibility, or privacy for speed.
- • and evidence quality: must pass before scoring other criteria.
- • User need and effectiveness: highest scored criterion.
- • Time, cost, and ease of use: compare only after and effectiveness pass.
Test evidence: For each option, record the E1-E3 result that supports or fails each criterion. Do not assign a score without a named observation.
- Version or option tested
- Criterion met or missed
- Evidence ID and result
- Revision made
- Reason for the revision
- Need and user
- Criteria and constraints
- Chosen option and evidence
- Test result
- Revision and reason
Students often think Students think the very first row returns is automatically the answer, and read as a grade rather than a comparison.. The trap: The best match is the hit with the highest and the lowest E-value together, not just whichever row sits on top, because can list a plausible-looking hit that is actually weak. Trusting position over the numbers gives a confident wrong ID.
Workflow: I pasted the unknown sequence into nucleotide BLAST at NCBI and ran the search. I annotated the screenshot to circle the top hit's organism name and percent identity.
Top hit (example values): Escherichia coli, percent identity 99 percent, E-value 2e-120.
Control run: I ran the teacher's known control sequence and it returned its expected organism at high identity, which confirms the tool and my workflow are working.
Identification statement: The unknown sample is most likely Escherichia coli, based on the top hit at 99 percent identity and a very low E-value.
| Organism (top hits) | Percent identity | E-value |
|---|---|---|
| Escherichia coli | 99% | 2e-120 |
| Shigella flexneri | 95% | 4e-90 |
| Salmonella enterica | 88% | 1e-60 |
This model shows the level of evidence and organization needed to complete: An annotated screenshot of your nucleotide BLAST hit table showing the top organism and percent identity, a one-sentence identification, and the result of your control run.
- State the question and method.
- Present the observations and data with units.
- Explain the result, limitations, and next investigation.
Keep the structure. Replace the question, facts, measurements, and evidence. Then recheck units, vocabulary, and whether the conclusion goes beyond the evidence.
Also due today: Upload screenshot to portfolio; bring notebook to Thursday's analysis session.
- 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.
Tap the speaker to hear a term. Add two of these to your notebook glossary with a definition and an example in your own words.
Pick just 2 or 3 words from today and make them yours: write what each one means in your own words, name the context clue or evidence that helped, then give one example from what you actually did in BLAST computer lab. Try your own words first; the glossary is there if you get stuck. This is voluntary and counts as extra credit, so keep it short.
Saved on this device. Show Mr. Mendoza or add these to your notebook glossary to claim the extra credit.
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.
Check yourself · commit, then reveal▸
Claim ceiling for this check: The supplied lesson evidence can support an observation, pattern, classroom mechanism, or next-step decision about computer lab. It cannot by itself prove causation, establish a real clinical diagnosis, or justify action outside this classroom task.
Your control run was a sequence you already knew was E. coli, but BLAST returns a top hit of Salmonella at 88 percent identity. What does this tell you, and should you trust today's unknown result?
Write an answer and pick a confidence to unlock the key.
Fast retrieval with instant answers, not the commit-then-reveal check above. Try each from memory first: write what you remember about the earlier units, then check yourself here.
Go further and get help▸
I can name the procedure's purpose and the evidence I will record. I can identify each named hazard and the control that reduces it: No biological materials in this session; standard computer lab rules apply. My data table is ready before materials are handled.
Finish the checklist before you handle any material.
- • No biological materials in this session; standard computer lab rules apply.
- • Do not close the BLAST results page before you screenshot it. Use Cmd+Shift+4 (Mac) or the Snipping Tool (Windows) to capture.
- • Save your screenshot to your portfolio folder right away, not just to the desktop.
- 1Before materials are handled, identify the purpose, variables or comparison, controls, measurement units, and stop-work condition.
- 2Copy the unknown DNA sequence from the case file into a scratch document so you do not lose it.
- 3Go to NCBI BLAST, choose nucleotide BLAST, and paste your sequence into the query box.
- 4Run the search, then read the top hit's organism name and percent identity.
- 5Take a screenshot of the hit table for your portfolio.
- 6Run a control sequence the teacher provides to confirm the workflow behaves.
- 7Write one sentence naming the likely organism and the evidence behind it.
- 8Record each result in the prepared table before interpreting it. Mark missing, repeated, or invalid results truthfully.
- 9Complete the named cleanup and waste route, remove PPE safely, wash hands when required, and confirm the station is ready for the next group.
| Trial or sample ID | Independent condition | Measured result with units | Observation before interpretation | Quality-control note |
|---|---|---|---|---|
Before the procedure, predict the result and cite the rule behind the prediction.
After the procedure, compare the result with the prediction and name one limitation or source of uncertainty.
What today's skills lead to. These are real health-science careers this course builds toward. Tap one to see, on the US Department of Labor's O*NET site, what the job actually involves, what it pays, and how fast it is growing.
If you miss the computer lab, run the same unknown sequence through the public NCBI web tool from home, screenshot the hit table, and submit your top-hit identification.
NCBI BLAST (web)Then submit your Lab report. Turn this in at the drop folder with your district Microsoft sign-in, or hand it to Mr. Mendoza in class. Both count as submitted. Doing the activity in myPLTW does not.
Class still runs. Complete the online activity above (it's self-guided). Need the concept taught without a teacher? Use this authoritative explainer:
NCBI BLAST- CompleteEvery required part of the artifact is present, nothing left blank.
- AccurateThe science and the data are correct and match the evidence.
- Scientific reasoningYou explain your claim with evidence and reasoning (CER), not just an answer.
- Professional communicationClear, organized, labeled, and written the way a clinician or scientist would.
- SubmittedTurned in the right way, on the class site or handed to Mr. Mendoza in class, and confirmed. Not in Schoology: that is where the report-card grade appears later.
- Error analysis and method · counts doubleName a specific limit of the method and how it moved your result, and compare what you predicted to what happened. "Human error" does not count; say what about the procedure or instrument caused it.