DNA Subway Flashcards

Questions and Answers

What are the three main stops in DNA Subway?

Delete sequences

Add sequences (correct)

Assemble sequences (correct)

Analyze sequences (correct)

What are the 4 steps of Assemble Sequences?

Sequence viewer, sequence trimmer, pair builder, and consensus builder.

What does a chromatogram give you?

Base call, quality score, sequence length, and which ddNTP was incorporated.

What is the goal of the Sequence Viewer?

To determine whether the sequence looks 'good'. Signup and view all the answers

What is the goal of the Sequence Trimmer?

To trim off low quality base calls from 5' and 3' ends of reads. Signup and view all the answers

What is the goal of the Pair Builder?

It links and aligns the forward and reverse reads. Signup and view all the answers

What is the goal of the Consensus Builder?

Compared and combined forward and reverse reads to get longer, more accurate DNA sequence. Signup and view all the answers

What do you need to build a phylogenetic tree from barcodes?

Known barcodes of closely related species and known barcodes of distantly related species for comparison. Signup and view all the answers

What are the main steps in 'Add Sequences'?

BLASTN, upload data, and reference data. Signup and view all the answers

What is the goal of BLASTN?

To find known DNA sequences that most closely match my barcode. Signup and view all the answers

What is the Bit Score based off of?

The alignment length and number of mismatches. Signup and view all the answers

What is the Expected Value in BLASTN results?

The likelihood that the match BLAST made between our query sequence and your match could happen by chance. Signup and view all the answers

How is alignment length determined?

By how long of a stretch of nucleotides match between my sequence and the database sequence. Signup and view all the answers

What is the wanted % of number of mismatches?

Below 1%. Signup and view all the answers

What is the wanted number of bases for Alignment length?

More than 400 bases. Signup and view all the answers

What is the goal of the final major step of DNA Subway?

Choose DNA sequences to compare and create a phylogenetic tree of the sequences chosen. Signup and view all the answers

What is the consensus sequence in MUSCLE Alignment?

It shows the most common nucleotide at each position. Signup and view all the answers

How are NJ Trees described?

Are simpler but less accurate. Signup and view all the answers

How are ML Trees described?

Are more complex but more accurate. Signup and view all the answers

Study Notes

DNA Subway Overview

Three main stops in DNA Subway: assemble sequences, add sequences, analyze sequences.

Assemble Sequences Steps

Sequence Viewer: Checks if the DNA sequence appears "good."
Sequence Trimmer: Removes low quality base calls from both 5' and 3' ends of reads.
Pair Builder: Links and aligns forward and reverse DNA reads.
Consensus Builder: Combines forward and reverse reads for a longer, more accurate DNA sequence.

Chromatogram Insights

Displays base call, quality score, sequence length, and incorporated ddNTP.

Phylogenetic Tree Construction

Requires known barcodes of closely related and distantly related species for effective comparison.

Adding Sequences Steps

Key processes include BLASTN, data upload, and referencing data.

BLASTN Goals

Aims to identify known DNA sequences that closely match a given barcode.

BLASTN Results Metrics

Bit Score: Based on alignment length and number of mismatches.
Expected Value: Represents chance that a match occurred randomly, indicating reliability of the results.

Sequence Comparison Criteria

Alignment length determined by the extent of nucleotide matching between the query sequence and database.
Desired mismatch percentage is below 1%.
Minimum required bases for alignment length is over 400 bases.

Final Analysis Objectives

In the last step of DNA Subway, select DNA sequences for analysis and creation of a phylogenetic tree.

Alignment Techniques

MUSCLE Alignment: Generates a consensus sequence showing the most frequent nucleotide at each position.
NJ Trees: Simpler construction, less accuracy.
ML Trees: More complex, providing greater accuracy in results.

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Description

Test your knowledge of the DNA Subway process with these flashcards. Learn about the main stops, assembling sequences, and chromatogram details. Perfect for students looking to reinforce their understanding of DNA sequencing.