UNIT 3 Flashcards
1
Q
Sequencing Overlap in NGS
A
- Sequencing Overlap
- Fundamental concept in NGS
- Regions where reads share common sequences
- Importance
- Genome assembly
- Error correction
- Structural variant detection
- Quantitative analysis
- Phasing and haplotyping
- Coverage enhancement
- Mechanisms
- Overlap-Layout-Consensus (OLC)
- de Bruijn Graph Assembly
- Pairwise read alignment
- Multiple sequence alignment (MSA)
- Challenges
- Repetitive regions
- Sequencing errors
- Computational complexity
- Variable read length and quality
- Low coverage areas
- Structural variations
- Types
- Pairwise overlap
- Multiple overlap
- Forward-forward overlap
- Forward-reverse overlap
- Partial overlap
- Applications
- Genome assembly
- Transcriptome assembly
- Error correction
- Structural variant detection
- Metagenomics
- Phasing and haplotyping
- Variant calling
- Tools
- Assembly tools (SPAdes, CANU, ABySS)
- Alignment tools (BWA, Minimap2, BLAST)
- Error correction tools (LoRDEC, Pilon)
- Consensus building tools (Pilatus, ConFindr)
- Future Directions
- Multi-platform data integration
- Improved algorithms
- Real-time overlap analysis
- Machine learning
- Error models
- Nanopore and single-molecule innovations
- Conclusion
- Essential for NGS applications
- Enables accurate and reliable data analysis
- Ongoing advancements in tools and techniques
2
Q
Layout and Consensus in Genome Assembly
A
- Layout and Consensus
- Core concepts in genome assembly
- Part of Overlap-Layout-Consensus (OLC) approach
- Layout
- Arranging reads based on overlaps
- Graph construction
- Handling ambiguities
- Scaffolding
- Challenges: complexity, chimeric reads
- Consensus
- Deriving final sequence from overlapping reads
- Resolving conflicts
- Generating consensus sequence
- Polishing the assembly
- Importance: accuracy, error correction, biological insight
- Summary
- Layout and consensus form the backbone of OLC assembly
- Essential for reconstructing genomes from sequencing data
- Key steps in understanding genomic structure and variation
3
Q
Layout and Consensus in Genome Assembly
A
- Layout and Consensus
- Core concepts in genome assembly
- Part of Overlap-Layout-Consensus (OLC) approach
- Layout
- Arranging reads based on overlaps
- Graph construction
- Handling ambiguities
- Scaffolding
- Challenges: complexity, chimeric reads
- Consensus
- Deriving final sequence from overlapping reads
- Resolving conflicts
- Generating consensus sequence
- Polishing the assembly
- Importance: accuracy, error correction, biological insight
- Summary
- Layout and consensus form the backbone of OLC assembly
- Essential for reconstructing genomes from sequencing data
- Key steps in understanding genomic structure and variation
4
Q
Double-Barreled Shotgun Sequencing (Hypothetical)
A
- Double-Barreled Shotgun Sequencing
- A hypothetical term for enhanced shotgun sequencing
- Potential Interpretations
- Dual library preparation
- Bidirectional sequencing
- Paired-end shotgun sequencing
- Combined short and long reads
- Advantages
- Improved coverage, assembly, and accuracy
- Enhanced variant detection and haplotype phasing
- Better handling of complex regions
- Challenges
- Computational complexity
- Data integration
- Cost-effectiveness
- Future Directions
- Multi-platform data integration
- Enhanced algorithms
- Real-time sequencing
- Machine learning
- Cost reduction
- Conclusion
- Promising approach for genomic analysis
- Requires careful consideration and implementation
- Future advancements may further enhance its capabilities
5
Q
Double-Barreled Shotgun Sequencing (Hypothetical)
A
- Double-Barreled Shotgun Sequencing
- A hypothetical term for enhanced shotgun sequencing
- Potential Interpretations
- Dual library preparation
- Bidirectional sequencing
- Paired-end shotgun sequencing
- Combined short and long reads
- Advantages
- Improved coverage, assembly, and accuracy
- Enhanced variant detection and haplotype phasing
- Better handling of complex regions
- Challenges
- Computational complexity
- Data integration
- Cost-effectiveness
- Future Directions
- Multi-platform data integration
- Enhanced algorithms
- Real-time sequencing
- Machine learning
- Cost reduction
- Conclusion
- Promising approach for genomic analysis
- Requires careful consideration and implementation
- Future advancements may further enhance its capabilities
6
Q
BLAST vs. FASTA for Sequence Comparison
A
- BLAST vs. FASTA
- Tools for comparing sequences
- BLAST (Basic Local Alignment Search Tool)
- Faster, suitable for large datasets
- Heuristic approach, local alignments
- Uses word matching and extension
- FASTA
- Slower, more sensitive for weak similarities
- K-tuple matching and rescanning
- Global alignment
- Key Differences
- Speed and sensitivity
- Word size
- Database search strategy
- Alignment type
- Scoring and Evaluation
- Substitution matrices (BLOSUM62, PAM)
- Gap penalties
- E-value
- Applications
- Gene annotation and discovery
- Evolutionary studies
- Functional prediction
- Genome mapping
- Protein structure and function
- Choosing the Right Tool
- Consider speed, sensitivity, and specific application needs
- Experiment with both tools to determine the best fit
7
Q
PSI-BLAST (Position-Specific Iterated BLAST)
A
- PSI-BLAST
- Advanced version of BLAST
- Detects distant homology
- How it Works
- Initial BLAST search
- PSSM construction
- Iterative searching
- Convergence
- Position-Specific Scoring Matrices (PSSM)
- Captures conservation patterns
- Adapts based on alignments
- PSI-BLAST vs. BLAST
- Improved sensitivity for distant homologs
- Slower due to iteration
- Applications
- Distant homology detection
- Protein family classification
- Functional annotation
- Evolutionary studies
- Structure prediction
- Limitations
- False positives
- Requires high-quality initial hits
- Computational time
- Risk of over-iteration
- Conclusion
- Powerful tool for finding remote homologs
- Essential for bioinformatics research
8
Q
PSI-BLAST (Position-Specific Iterated BLAST)
A
- PSI-BLAST
- Advanced version of BLAST
- Detects distant homology
- How it Works
- Initial BLAST search
- PSSM construction
- Iterative searching
- Convergence
- Position-Specific Scoring Matrices (PSSM)
- Captures conservation patterns
- Adapts based on alignments
- PSI-BLAST vs. BLAST
- Improved sensitivity for distant homologs
- Slower due to iteration
- Applications
- Distant homology detection
- Protein family classification
- Functional annotation
- Evolutionary studies
- Structure prediction
- Limitations
- False positives
- Requires high-quality initial hits
- Computational time
- Risk of over-iteration
- Conclusion
- Powerful tool for finding remote homologs
- Essential for bioinformatics research
9
Q
PHI-BLAST (Pattern Hit Initiated BLAST)
A
- PHI-BLAST
- Specialized BLAST for pattern-based searches
- How it Works
- Input query and pattern
- Pattern matching
- BLAST search on pattern-hit sequences
- Return results
- Applications
- Functional annotation
- Domain and motif detection
- Enzyme classification
- Protein family studies
- Disease-associated motif identification
- Limitations
- Requires known pattern
- Limited scope
- Fewer results
- Pattern accuracy
- Speed
- Conclusion
- Valuable tool for targeted searches
- Essential for specific bioinformatics tasks
- Combines pattern matching and sequence alignment
10
Q
PROBE (Pattern Recognition of Biological Elements)
A
- PROBE
- Tool for identifying conserved patterns in sequences
- How it Works
- Input query sequence
- Pattern matching
- Database search
- Scoring matches
- Applications
- Functional annotation
- Evolutionary conservation studies
- Domain and motif discovery
- Comparative genomics
- Drug target identification
- Limitations
- Limited to known patterns
- Focus on patterns, may miss overall similarity
- Database dependency
- Slower performance
- Conclusion
- Valuable for identifying functional elements
- Essential for studying protein function and evolution
- Combines pattern recognition and sequence comparison
