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Questions and Answers
What is a non-redundant database?
What is a non-redundant database?
The Expect value (E) increases as the Score (S) of a match increases.
The Expect value (E) increases as the Score (S) of a match increases.
False
What does an alignment score represent?
What does an alignment score represent?
It represents a computed score based on matches, substitutions, insertions, and deletions in an alignment.
The percent of the query length included in the aligned segments is referred to as __________.
The percent of the query length included in the aligned segments is referred to as __________.
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Match the following terms with their definitions:
Match the following terms with their definitions:
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What is the main difference between pairwise alignment and multiple sequence alignment?
What is the main difference between pairwise alignment and multiple sequence alignment?
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The Smith-Waterman algorithm is primarily used for global alignment.
The Smith-Waterman algorithm is primarily used for global alignment.
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What graphical method is used to compare two biological sequences using dots?
What graphical method is used to compare two biological sequences using dots?
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A gap in sequence alignment represents a mismatch caused by an insertion or a ______ in the other sequence.
A gap in sequence alignment represents a mismatch caused by an insertion or a ______ in the other sequence.
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Match the following terms with their definitions:
Match the following terms with their definitions:
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What does the BLAST program primarily compare?
What does the BLAST program primarily compare?
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Dot-matrix diagrams can show gaps directly.
Dot-matrix diagrams can show gaps directly.
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Name the two main types of alignment methods discussed.
Name the two main types of alignment methods discussed.
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What is the primary goal of sequence alignment?
What is the primary goal of sequence alignment?
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Local sequence alignment examines the entire sequence from end to end.
Local sequence alignment examines the entire sequence from end to end.
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What algorithm is commonly used for global sequence alignment?
What algorithm is commonly used for global sequence alignment?
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Sequence alignment can help in identifying a species by finding ______ species.
Sequence alignment can help in identifying a species by finding ______ species.
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Which application of sequence alignment involves determining evolutionary relationships?
Which application of sequence alignment involves determining evolutionary relationships?
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Match the type of alignment to its definition:
Match the type of alignment to its definition:
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Mutations and variations can be detected by comparing two or more sequences.
Mutations and variations can be detected by comparing two or more sequences.
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Why might researchers want to predict protein secondary structure based on sequence?
Why might researchers want to predict protein secondary structure based on sequence?
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Study Notes
Sequence Alignment
- The process of comparing sequences by identifying regions of similarity, which may suggest functional, structural, or evolutionary relationships.
Applications
- Species identification: Determine species and find homologous species.
- Phylogeny: Create phylogenetic trees to determine evolutionary relationships.
- Mutation and Variation Analysis: Compare sequences to identify mutations and variations.
- Gene Finding: Use lengths of Open Reading Frames (ORFs) and alignment to reference genomes or similar organisms.
- Function Prediction: Predict gene function based on sequence similarity with known genes.
- Protein Secondary Structure Prediction: Predict secondary structure based on sequence, saving time and resources compared to experimental methods.
Types of Sequence Alignment
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Global Sequence Alignment: Aligning all characters (nucleotides or amino acids) across the entire length of the sequence. Useful for analyzing minor differences or polymorphisms like single nucleotide polymorphisms (SNPs)
- Algorithm: Needleman–Wunsch
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Local Sequence Alignment: Aligning regions of sequences with the highest density of matches, ignoring dissimilar regions. Useful for dissimilar sequences that have regions of similarity like motifs or domains.
- Algorithm: Smith–Waterman
Global vs Local Alignment
- Global Alignment: More amino acids can be aligned.
- Local Alignment: Stops at the end of regions with strong similarity or identity.
Pairwise vs Multiple Alignment
- Pairwise Alignment: Comparing two biological sequences.
- Multiple Sequence Alignment (MSA): Comparing three or more biological sequences.
Methods of Sequence Comparisons
- Dot-Matrix Diagram: A graphical method for comparing two sequences. Sequences are written horizontally and vertically, with dots marking shared characters. Diagonal lines represent regions of alignment.
- Optimal Alignment: Sequences are written in rows, with matching characters in the same column, mismatches in the same column, and gaps indicating insertions or deletions.
Gaps
- A mismatch in the alignment caused by an insertion or deletion in one of the sequences.
BLAST (Basic Local Alignment Search Tool)
- A program for comparing biological sequences (amino acids or nucleotides) to sequence databases.
BLAST Programs
- Blastn: Nucleotides vs. Nucleotides
- Blastp: Proteins vs. Proteins
- Blastx: Translated nucleotides vs. proteins
- tblastn: Proteins vs. Translated nucleotides
- tblastx: Translated nucleotides vs. Translated nucleotides
Retrieval from NCBI
- Submit a DNA or protein sequence (query sequence) to a database for alignment.
BLAST Databases
- Non-redundant Databases: Contain only one representative of identical sequences, reducing the number of matches.
BLAST Search Fields
- Additional parameters that can be used to refine the search like: "protease NOT hiv1[organism]", "1000:10000[slen]" (length of the sequence).
Nucleotide BLAST vs Protein BLAST
- Nucleotide BLAST: Aligns nucleotide sequences by finding short substrings (words).
- Protein BLAST: Aligns protein sequences using a scoring matrix that accounts for amino acid similarities.
BLAST Results
- Alignment Score: A score based on matches, substitutions, insertions, and deletions within the alignment.
- Max Score: The highest alignment score between the query sequence and the database segment.
- Total Score: The sum of scores for all aligned segments. Higher scores indicate better alignment, but lower E-values.
- Query Coverage: The percentage of the query length that is included in the aligned segments.
- Expect Value (E-value): The number of hits expected by chance when searching a database of a certain size. Decreases exponentially with increasing score, suggesting higher significance.
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Description
Explore the concept of sequence alignment and its significance in fields such as species identification, phylogeny, and gene function prediction. This quiz covers global sequence alignment techniques and their applications in analyzing mutations and variations. Test your knowledge on how these methods help in evolutionary studies and protein structure prediction.
