Adapting Lab Courses for Virtual Learning on Benchling

Problem-Based Learning Module: In Silico Analysis of DNA and Protein Sequences

Fundamental in silico analysis is often used in molecular biology research but it can be challenging to teach in laboratory courses. This is often due to complex analysis, which can be challenging for students to pick up. Benchling makes these analyses more accessible to students by simplifying multiple tools into a web interface that help students answer scientific questions and collect insights. Our example discusses a way for students to grasp introductory principles of bioinformatics by performing sequence alignments and BLAST searches for DNA sequences. Meanwhile, they will acquire deductive reasoning skills.

Student Learning Outcomes

1 / Learn basic principles of sequence analysis as an introduction to bioinformatics

2 / Translate DNA sequences into protein sequences

3 / Infer DNA and protein sequence homology through alignments

4 / Create a consensus sequence from a given set of sequences

Getting This Module Started on Benchling

1. Import DNA sequences for five different genes into Benchling and ensure some sequences belong to a known gene family. Remove any identifying information or annotations and relabel these sequences as ‘Unknown A,” “Unknown B”, and so on.

2. Inform your students that these sequences were collected “experimentally” and that they will use them as a starting point for in silico analysis.

3. Within a Notebook template, link these five sequences and provide a set of analyses you want the students to perform on them. For example, you might have them perform DNA sequence alignment, DNA-to-protein translation, and protein sequence creation and alignment.

4. Based on their analyses, ask students to determine which sequences are likely homologous. Have them create and store a consensus sequence in DNA and protein formats using the homologous sequences.

5. Finally, have them open all five unknown sequences and perform a NCBI BLAST search in Benchling to assess if they have been observed in nature. Ask them to annotate these sequences in Benchling with accession ID and organism.

6. From NCBI, ask students to investigate the accession IDs for all five sequences and classify each a known gene, putative gene, or unknown gene.

7. Have students create a table in a Notebook entry compiling all sequences (with hyperlinks) and related information. They should submit the Notebook entry for assessment.

Tools and Analysis within Benchling

• Sequence imports from external databases or various file formats

• DNA and protein sequence alignments

• NCBI BLAST searches for DNA sequences

• Sequence annotation