BLAST computer lab
Open your materials, follow the steps, then turn in your work.
Document a nucleotide BLAST workflow and explain what the resulting sequence comparison can and cannot support.
1. Open your materials
Use the materials named in the first step below. Open lesson resources.
2. Start the work
Open Activity 1.1.3, Outbreak Investigation Day 2 and Automated DNA Sequence Data from the PLTW hub. Read the Day 2 context. Use the parent PDF's physical pages 8–9 for Part II steps 6–8 and its color/ambiguity key.
Show all 6 required steps
- Open Activity 1.1.3, Outbreak Investigation Day 2 and Automated DNA Sequence Data from the PLTW hub. Read the Day 2 context. Use the parent PDF's physical pages 8–9 for Part II steps 6–8 and its color/ambiguity key.
- Read the assigned trace in numbered order, not by page position. Lane 1 is on the right; lane 2 is on the left. Keep a continuous readable segment and mark uncertainty using the parent key. Save the input and its position range.
- Follow the separate Part III tutorial on physical pages 16–30. Use its page 18 input for the workflow check. Record the actual database and program settings and what happened; do not claim a prescribed result.
- Use Part IV steps 10–12 on physical pages 31–32 for the trace-derived comparison. A query is the sequence you submit; the selected database is the reference collection it searches. Save the chosen settings with the result.
- Save a hit-table screenshot. Label the compared hit, percent identity, query coverage and E-value where shown. Write one qualified comparison sentence and record the tutorial workflow-check outcome, including failure or uncertainty.
- Discuss the result and its limits with a partner. Submit official records and the separate one-PDF lab report to their own assignments. Stop at the day's assigned portion; bring the saved result or partial record to Tuesday.
Lost your place? Find your saved step, input source and settings. Reopen the matching parent page: trace/key pages 8–9, tutorial pages 16–30, or trace-derived search pages 31–32. If blocked, keep a partial record and ask a specific question.
Check your work before submitting
- Use the assigned trace, parent key and tutorial without substituting Friday's illustrative read.
- Explain percent identity as matching aligned positions, alongside coverage and E-value.
- Keep the official records and report separate; record actual results and unresolved steps honestly.
3. Turn in your work
DueCheck Schoology- Hand in
- Lab report: annotated hit-table screenshot, one-sentence qualified comparison, and actual tutorial workflow-check result.
How to submit and name your file
Keep two assignments separate. Submit the assigned official activity records to PLTW Work (8520302449). Submit the lab report as one PDF to Lab report (8520302481); if the paper report was collected in class, do not upload it again.
In Schoology, open your course and the assignment for this lesson. Attach your file, select Submit, and check that it appears in the submission.
PDF upload helpYou get two school days for every day you were absent, so this deadline moves with you.
Find this lesson's Schoology assignments
These are existing assignments for your section. Follow the directions in the assignment you are working on; this list does not add new work. Check Schoology for each deadline.
Link will not open? Open Schoology, choose your course and section, and find the title shown above.
How this lesson connects
Friday: a read reports base order. Today: document the comparison and its limits. Tuesday: compare coverage and E-value alongside identity.
Thinking practice for this week▸
Reasoning: connecting evidence to the claim
What separates sound reasoning from bad reasoning, and how do you check your own?
Reasoning is the part where you explain why your evidence supports your claim. It is the bridge. Without it, a claim and some data are just sitting next to each other; reasoning shows how the data leads to the conclusion, often using a scientific principle.
Good reasoning is logical (each step follows from the last), it actually uses your evidence (not just restates the claim), and it considers alternatives (could the data mean something else?). Bad reasoning leans on logical fallacies: jumping to conclusions, confusing correlation with causation, or attacking the person instead of the idea.
Check your own reasoning by trying to break it: state the opposite and see if your evidence rules it out. Ask “what would have to be true for me to be wrong?” If you cannot answer, your reasoning is not finished yet.
- • Logical: each step follows from the one before it.
- • Grounded: it uses your evidence, and names the principle that links it to the claim.
- • Fair: it considers other explanations and says why yours is better.
- • Self-checked: you tried to prove yourself wrong and could not.
- • Correlation is not causation: two things moving together does not mean one caused the other.
- • Hasty generalization: one case does not prove a rule.
- • Ad hominem: attacking the person, not their evidence.
Write the reasoning that links your evidence to your claim from earlier this week. Then write the strongest objection to it, and answer that objection.
Need help? Warm-up, timing, and directions▸
💡 Big idea: compares a read with reference sequences. A match supports a limited comparison, not proof of identity or disease causation.
- 0-10 minRecall Friday's base-order idea; open the three official resources and locate the trace key and today's stopping point
- 10-25 minComplete Part II steps 6–8: read the assigned trace with its key, retain uncertainty and save the chosen continuous segment
- 25-45 minFollow the Part III tutorial as the check; record settings and actual outcome, asking for help if blocked
- 45-60 minComplete Part IV steps 10–12 using the trace-derived query; save the result and selected settings
- 60-72 minLabel the hit-table screenshot, draft one qualified comparison sentence and record the actual -check outcome
- 72-80 minDiscuss limits with a partner; submit official records and the separate report, or retain a truthful partial record and specific help request
- • Use the official Day 2 context, trace and parent directions together.
- • Today's assigned portion: Part II steps 6–8, the Part III tutorial, and Part IV steps 10–12. Stop after recording and discussing the trace-derived comparison. Later disease research and conclusion questions are not assigned today.
- • The tutorial and trace-derived search have different roles. Keep both records.
- • Save unresolved work honestly. Record the attempted step and ask for specific help.
- • compares a read with reference sequences. A match supports a limited comparison, not proof of identity or disease causation.
- • : The percentage of aligned positions that match exactly. It is not the percentage of your whole query covered or a confidence score.
- • The Activity 1.1.3 tutorial is our check: check copying, selected settings and reading the output. It is not a biological control and does not validate the case identification.
PLTW connection and today's work
Open Activity 1.1.3 Using DNA to Identify Pathogens and its Day 2 and Automated DNA Sequence Data resources in the PLTW hub.
Today's stopping point: Bring Friday September 11's sequencing summary and question. Today's stopping point does not complete the full official activity.
PLTW activity titles identify the course connection. If your account will not open, use the posted materials for today and tell Mr. Mendoza. Do not mark an online activity complete unless you completed it.
Course connection
- Activity 1.1.3 Using DNA to Identify Pathogens
Today has two assignments: official activity records and the separate one-PDF report. Use their named links. Do not submit either twice.
Show another explanation or a smaller first step
Need help? Choose a starting point
Lesson resources: reading, slides, and vocabulary▸
Use the deck and optional guided notes to support the two assignments above. No extra exit ticket or group product is due.
Generated from this lesson's canonical data with a red-team citation check.
A sequencing read reports the order of DNA bases in a sample; comparing that order with reference sequences is what can name an organism, and the naming still depends on the quality of the read and of the comparison.
compares a read with reference sequences. A match supports a limited comparison, not proof of identity or disease causation.
Driving question: How can you document a search so another person can check the input, settings, result and limits?
What you already know: Friday September 11: a read reports DNA base order. The letters alone do not establish read quality or name an organism.
New idea: compares a read with reference sequences. A match supports a limited comparison, not proof of identity or disease causation.
Visual or model: F1. F1. Original guide to organizing the search record. No sequence or result is supplied here. What to notice: Keep input, settings, result and interpretation separate.
- Open Activity 1.1.3, Outbreak Investigation Day 2 and Automated Data from the PLTW hub. Read the Day 2 context. Use the parent PDF's physical pages 8–9 for Part II steps 6–8 and its color/ambiguity key.
- Read the assigned trace in numbered order, not by page position. Lane 1 is on the right; lane 2 is on the left. Keep a continuous readable segment and mark uncertainty using the parent key. Save the input and its position range.
- Follow the separate Part III tutorial on physical pages 16–30. Use its page 18 input for the check. Record the actual database and program settings and what happened; do not claim a prescribed result.
- Use Part IV steps 10–12 on physical pages 31–32 for the trace-derived comparison. A query is the sequence you submit; the selected database is the reference collection it searches. Save the chosen settings with the result.
- Save a hit-table screenshot. Label the compared hit, , and E-value where shown. Write one qualified comparison sentence and record the tutorial -check outcome, including failure or uncertainty.
- Discuss the result and its limits with a partner. Submit official records and the separate one-PDF lab report to their own assignments. Stop at the day's assigned portion; bring the saved result or partial record to Tuesday.
Real biomedical example: Sequence similarity is evidence to interpret with read quality, coverage and reference limits, not proof of a disease cause. Source: BLAST FAQ: interpreting similarities and limitations.
What the evidence supports: The official resources supply the input and tutorial. Your own saved result supplies the comparison evidence. The original guide and check cards organize the work.
What it cannot prove: A sequence match and tutorial check cannot prove identity or disease causation.
- • Query: The sequence you submit for a search. Keep its source and position range with your record.
- • Database: The selected collection of reference sequences. It does not contain every possible organism or sequence.
- • Hit and : A hit is a returned reference match whose shows which positions were compared with your query.
- • : The percentage of aligned positions that match exactly. It is not the percentage of your whole query covered or a confidence score.
- • : The percentage of your query included in the . A short match may leave much of the query untested.
- • E-value: The expected number of matches this good by chance in the searched database. Smaller is stronger similarity evidence, not proof of a diagnosis.
- • check: The official tutorial used to check copying, settings and output reading. Record what happened; it does not prove the unknown's identity.
Use it now: Locate the input source and settings in your own record, then revise the existing comparison sentence to state what remains uncertain.
Go further, optional: NCBI's FAQ explains database and interpretation limits. Additional disease research and full-activity conclusions are outside today's assigned portion.
searches the selected reference collection. Identity describes matching aligned positions; coverage shows how much of the query aligned. Neither alone establishes a diagnosis.
Limit: compares a read with reference sequences. A match supports a limited comparison, not proof of identity or disease causation.
Use the official trace with the parent key on pages 8–9. The separate tutorial on pages 16–30 checks the . Use pages 31–32 for the trace-derived comparison.
Limit: These are input and procedure locators, not a saved result. Never substitute Friday's illustrative read.
Keep assigned official records separate from the one-PDF report: labeled screenshot, qualified sentence and actual -check result. Record unresolved work and request help.
Limit: No prescribed search result and no claim that a partial record completes the report.
MI search-record rehearsal · Source-entry rehearsal
Your role: student checking the same report
Decision: Which wording fits the record you actually have? Use this discussion to revise the existing report, not to create another submission.
- • Report a limited comparison from the saved result and its settings.
- • Treat the top hit as proof of identity and disease causation.
- • Record the failed step and ask for help instead of inventing a result.
Response: Keep two assignments separate. Submit the assigned official activity records to PLTW Work (8520302449). Submit the lab report as one PDF to Lab report (8520302481); if the paper report was collected in class, do not upload it again.
Claim ceiling: A sequence match and tutorial check cannot prove identity or disease causation.
Students often think The first hit or a high proves which organism caused the illness.. The trap: A matching aligned region is limited by read quality, coverage and the selected reference collection. The check does not establish a disease cause.
Writing frame, not a completed result:
Input: [official trace position range]. Settings: [actual database and program].
Screenshot: [attach your own labeled hit table].
Comparison: [reference hit] is a possible match to [the aligned region], based on [actual identity and coverage]; [specific uncertainty] remains.
Workflow check: [tutorial step, settings and actual outcome].
If no result exists, record the attempted step and the help needed. Do not fill the blanks with invented values.
This blank frame helps organize your own recorded results for: Lab report: annotated hit-table screenshot, one-sentence qualified comparison, and actual tutorial workflow-check result.
- Open Activity 1.1.3, Outbreak Investigation Day 2 and Automated DNA Sequence Data from the PLTW hub. Read the Day 2 context. Use the parent PDF's physical pages 8–9 for Part II steps 6–8 and its color/ambiguity key.
- Read the assigned trace in numbered order, not by page position. Lane 1 is on the right; lane 2 is on the left. Keep a continuous readable segment and mark uncertainty using the parent key. Save the input and its position range.
- Follow the separate Part III tutorial on physical pages 16–30. Use its page 18 input for the workflow check. Record the actual database and program settings and what happened; do not claim a prescribed result.
- Use Part IV steps 10–12 on physical pages 31–32 for the trace-derived comparison. A query is the sequence you submit; the selected database is the reference collection it searches. Save the chosen settings with the result.
- Save a hit-table screenshot. Label the compared hit, percent identity, query coverage and E-value where shown. Write one qualified comparison sentence and record the tutorial workflow-check outcome, including failure or uncertainty.
- Discuss the result and its limits with a partner. Submit official records and the separate one-PDF lab report to their own assignments. Stop at the day's assigned portion; bring the saved result or partial record to Tuesday.
Keep your actual input, settings and results. If work is unresolved, record the attempted step and ask for help. Do not invent or substitute results.
Also due today: Keep two assignments separate. Submit the assigned official activity records to PLTW Work (8520302449). Submit the lab report as one PDF to Lab report (8520302481); if the paper report was collected in class, do not upload it again.
- 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.
Practice: try a question, then check your answer▸
Claim ceiling for this check: A sequence match and tutorial check cannot prove identity or disease causation.
Your tutorial search runs successfully. Does that alone establish the identity of the trace-derived sample or its role in disease?
Write an answer and pick a confidence to unlock the key.
Missed class or ready for more?▸
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 a file will not open or a search fails, save your settings, the step attempted and any error message. Write the specific help you need. Keep this partial record and ask Mr. Mendoza how to continue; it is not a completed report or a replacement result.
Official resources and parent page locatorsKeep two assignments separate. Submit the assigned official activity records to PLTW Work (8520302449). Submit the lab report as one PDF to Lab report (8520302481); if the paper report was collected in class, do not upload it again.
Class still runs. Complete the online activity above (it's self-guided). Need the concept taught without a teacher? Use this authoritative explainer:
Official inputs: parent directions, Day 2 context and traceHow I will check this work
- Use the assigned trace, parent key and tutorial without substituting Friday's illustrative read.
- Explain percent identity as matching aligned positions, alongside coverage and E-value.
- Keep the official records and report separate; record actual results and unresolved steps honestly.
BLAST compares a read with reference sequences. A match supports a limited comparison, not proof of identity or disease causation. Use the Schoology assignment linked above to submit it.
This week
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