Bioinformatics Lecture 6: BLAST Principles

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Questions and Answers

What is the primary function of identifying paralogs and orthologs in bioinformatics?

Discovery of new genes

Nucleotide sequence formatting

PCR primer selection

Exploration of protein function or amino acid residues (correct)

BLASTP searches can only identify protein sequences in prokaryotic organisms.

False

What does the FASTA format begin with in its description line?

The purpose of using the new Core_nt BLAST database is to reduce __________ for highly represented organisms.

redundancy Signup and view all the answers

Match the following sequences with their corresponding descriptions:

FASTA format = Begins with a '>' sign BLASTP search = Compares a protein sequence against a database Paralog = A gene related by duplication Accessing NCBI = Using an accession number or FASTA format Signup and view all the answers

What is the primary function of a High Scoring Segment Pair (HSP) in BLAST searching?

To provide a local alignment with no gaps Signup and view all the answers

E-values and S-scores are key factors in determining the significance of a BLAST search result.

True Signup and view all the answers

What does the acronym BLAST stand for?

Basic Local Alignment Search Tool Signup and view all the answers

What does raising the word size threshold in a sequence alignment process primarily affect?

Increases the speed of the alignment process Signup and view all the answers

High-scoring Segment Pairs (HSPs) result from matching K-mers being extended into stretches.

True Signup and view all the answers

In BLAST searching, K-mers are words that match with a score above a selected threshold (T), and these are extended to form a ______.

High Scoring Segment Pair (HSP) Signup and view all the answers

What is the scoring system used in BLASTP for matches and mismatches?

+2 for a match and -3 for a mismatch Signup and view all the answers

Match the following BLAST components with their functions:

E-value = Measures the expected random matches S-score = Indicates the alignment quality HSP = Local alignment without gaps K-mer = Word size used in sequence alignment Signup and view all the answers

Which of the following is true about BLASTP search parameters?

It compares protein sequences against a protein database Signup and view all the answers

The primary purpose of the BLASTP search is to identify _ and _ between protein sequences.

similarities, variations Signup and view all the answers

Match the following terms with their correct descriptions:

Paralog = Genes that arise by duplication Ortholog = Genes that are derived from a common ancestral gene BLASTP = Protein alignment tool FASTA = A text-based format for representing nucleotide sequences Signup and view all the answers

FASTA format and usage are unrelated to BLAST searching.

False Signup and view all the answers

Describe one method for nucleotide discovery in bioinformatics.

Sequencing technologies like Sanger sequencing or Next-Generation Sequencing (NGS). Signup and view all the answers

In Phase 3 of the sequence alignment process, which method is applied to ensure statistical significance?

Composition-based statistics Signup and view all the answers

Raising the word size from w=11 to w=15 will yield more matches.

False Signup and view all the answers

What are the two main types of alignments that BLAST performs?

Global and Local alignments Signup and view all the answers

Study Notes

Learning Outcomes

Ability to describe functions of BLAST search.
Familiarity with main BLAST programs and their applications.
Understanding of BLAST operational mechanisms.
Definition and significance of High Scoring Segment Pair (HSP).
Explanation of E-values and S-scores relevance.
Discussion of BLAST alternatives and advancements.
Comparison of BLAST and FASTA search methodologies.
Capability to conduct a BLAST search with a query sequence.

High-Scoring Segment Pair (HSP)

HSP is the fundamental unit of BLAST; represents local alignment with no gaps.
Involves two sequence fragments of equal length with a local maximum alignment score.
Alignments must meet or exceed a defined cutoff score to qualify as HSP.
Defined by two sequences, a scoring system, and a cutoff score.
K-mers (word matches) that exceed a selected threshold (T) are extended to form HSP.

How BLAST Works

Phase 1: Compile a list of high-scoring "words" from the query sequence.
Phase 2: Scan the database for matches and extend to form HSPs.
Phase 3: Traceback to evaluate and generate a gapped alignment, calculating insertions and deletions.

Uses of BLAST Searches

Identifies functions of paralogs and orthologs.
Explores protein functions or specific amino acid residues.
Assists in discovering new genes or determining gene presence in organisms.
Evaluates Expressed Sequence Tags (ESTs) and gene/protein variants.
Aids in PCR primer selection for specialized databases.

Query Sequence Format

Query input can be a FASTA format sequence or an NCBI accession number.
FASTA format starts with a '>' character followed by sequence data in uppercase or lowercase letters.

BLAST Database and Search Enhancements

New Core_nt database improves search speed and efficiency by reducing redundancy.
Enables faster searches and easier data handling for standalone BLAST implementations.
BLAST scoring systems may vary (e.g., match: +2, mismatch: -3 for BLASTN).

Phase Details

Phase 1 emphasizes the initial compilation of word sequences for high scores.
Phase 2 focuses on extending exact matches into HSPs.
Phase 3 involves applying statistical methods for calculating alignments while tracing back to maintain integrity in results.

Scoring and Performance Considerations

Adjusting the word size can affect speed and match frequency; larger word sizes result in faster searches with fewer hits.
Smaller word sizes yield more hits but may slow down the search process.

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Description

This quiz covers the principles of BLAST searching in bioinformatics as discussed in BIOC 3265. You will learn about the functions of BLAST, its main programs, and key concepts such as High Scoring Segment Pairs and statistical measures like E-values and S-scores. Additionally, the quiz will touch on alternatives to BLAST to enhance your understanding.