Genome Browsers Overview Quiz
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Questions and Answers

What does ClinVar primarily focus on?

  • Nucleotide database management
  • Publicly submitted variations and observations of diseases (correct)
  • Gene expression studies
  • Automated data extraction tools

    • Which of the following is a database that contains information on single nucleotide polymorphisms?

  • GEO
  • Genomic Data Commons
  • dbSNP (correct)
  • Ensembl

    • Which resource is known for containing hundreds of thousands of expression experiments?

  • GEO (correct)
  • PubMed
  • NCBI
  • ClinVar

    • What is the significance of the star rating in ClinVar results?

    <p>It indicates the level of confidence in the results</p> Signup and view all the answers

    What is one potential drawback of using the NCBI extraction tools?

    <p>They can be overly complicated</p> Signup and view all the answers

    Which of the following links to a faster European mirror site for genomic data?

    <p><a href="http://genome-euro.ucsc.edu">http://genome-euro.ucsc.edu</a></p> Signup and view all the answers

    What does the acronym GEO stand for?

    <p>Gene Expression Omnibus</p> Signup and view all the answers

    What is a feature that UCSC Genome Browser offers for exploring gene data?

    <p>Track Viewing</p> Signup and view all the answers

    What feature makes Ensembl particularly useful for data extraction?

    <p>Automated extraction tools</p> Signup and view all the answers

    What does the 'zoom in by factor of 3X' feature enable a user to do?

    <p>Increase the detail of visible genetic data</p> Signup and view all the answers

    Which database is specifically known for providing standardized clinical significance of genetic variants?

    <p>ClinVar</p> Signup and view all the answers

    What does the direction of the arrows in a gene representation indicate?

    <p>The gene is on the reverse (3' to 5') strand</p> Signup and view all the answers

    What distinguishes GRCh38 from GRCh37 in the UCSC Genome Browser?

    <p>GRCh38 has fewer gaps and newer annotations.</p> Signup and view all the answers

    What tool does Ensembl provide for data extraction that is not covered in UCSC?

    <p>Table Browser</p> Signup and view all the answers

    How can a user highlight a specific region for zooming?

    <p>By dragging the mouse over the scale or chromosome track</p> Signup and view all the answers

    What type of analysis can gnomAD provide when looking up variants?

    <p>Minor allele frequency and clinical significance</p> Signup and view all the answers

    What information can be accessed by clicking on a transcript?

    <p>A page describing the transcript and links to resources</p> Signup and view all the answers

    Which browser would be best for database queries related to genomic data?

    <p>NCBI</p> Signup and view all the answers

    What is the purpose of the UCSC tracks feature?

    <p>To organize data by types such as Mapping and Genes</p> Signup and view all the answers

    What functionality does the 'Zoom in/Zoom out' feature provide in the UCSC browser?

    <p>Focusing on a specific genomic region</p> Signup and view all the answers

    What can be observed when zoomed in to the level of DNA and amino acids?

    <p>All six coding frames, three forward and three reverse</p> Signup and view all the answers

    Which is NOT a part of the anatomy of the UCSC Genome Browser?

    <p>Variant classifications</p> Signup and view all the answers

    What do the coordinates chr11:110,045,605-110,767,437 represent?

    <p>The position of a protein coding gene on chromosome 11</p> Signup and view all the answers

    What happens when a user mouses over an exon?

    <p>The corresponding intron number is displayed</p> Signup and view all the answers

    What programming languages are mentioned as having a REST API for data extraction?

    <p>Perl and Java</p> Signup and view all the answers

    What type of data structure is indicated by the term 'lookup'?

    <p>Dictionary</p> Signup and view all the answers

    What is the primary biotype of the BRCA2 gene as described in the lookup?

    <p>protein_coding</p> Signup and view all the answers

    Which gene is associated with Bardet-Biedl syndrome according to the database lookup?

    <p>BBS2</p> Signup and view all the answers

    What assembly name is indicated for the genes mentioned?

    <p>GRCh38</p> Signup and view all the answers

    In the example provided, what is used to retrieve information about multiple gene symbols?

    <p>symbol_post</p> Signup and view all the answers

    What is the display name for the BRCA2 gene as mentioned in the lookup output?

    <p>BRCA2</p> Signup and view all the answers

    What does the strand value of BRCA2 indicate in the lookup result?

    <p>1 (positive)</p> Signup and view all the answers

    Which of the following is NOT a gene symbol mentioned in the content?

    <p>BBS5</p> Signup and view all the answers

    What is the description output for the BRCA2 gene?

    <p>BRCA2 DNA repair associated</p> Signup and view all the answers

    What type of biotype is BBS4 classified as?

    <p>protein_coding</p> Signup and view all the answers

    What is contained in the 'description' field for BBS4?

    <p>Bardet-Biedl syndrome 4 [Source: HGNC Symbol; Acc: HGNC:969]</p> Signup and view all the answers

    Which server is used to obtain the cDNA for the transcript_id?

    <p><a href="http://rest.ensembl.org">http://rest.ensembl.org</a></p> Signup and view all the answers

    What does the variable 'transcript_id' contain after processing from the lookup?

    <p>ENST00000380152</p> Signup and view all the answers

    What is the value of the 'display_name' field for BBS4?

    <p>BBS4</p> Signup and view all the answers

    Which of the following fields indicates the genomic range of BBS4?

    <p>start and end</p> Signup and view all the answers

    What type of molecule is represented in the sequence obtained for the transcript_id?

    <p>dna</p> Signup and view all the answers

    How is the response from the REST API request formatted for the sequence?

    <p>text/x-fasta</p> Signup and view all the answers

    What was the conclusion of the 2017 review regarding first-generation GM crop animal feed?

    <p>There is no clear evidence of adverse effects on animal health.</p> Signup and view all the answers

    What effect would switching to non-GMO animal feed have according to research by Iowa State University?

    <p>Increase greenhouse gas emissions and food prices.</p> Signup and view all the answers

    What modern agricultural technique has been used for the last 100 years to create new crop varieties?

    <p>Mutation breeding using chemicals or radiation.</p> Signup and view all the answers

    How many studies have been conducted examining the health and environmental safety of GMO crops?

    <p>Over 3,000 studies.</p> Signup and view all the answers

    What is a potential consequence of continued use of GMO crops without proper assessment?

    <p>Emergence of resistant pest species.</p> Signup and view all the answers

    How many processed pseudogenes are mentioned in the database?

    <p>Approximately 10,668</p> Signup and view all the answers

    What is the main goal of the Earth BioGenome Project?

    <p>To sequence the genomes of all known eukaryotic species</p> Signup and view all the answers

    Which of the following is a characteristic of non-processed pseudogenes?

    <p>They are not translated into proteins.</p> Signup and view all the answers

    What is the approximate size of the Y chromosome in the human genome?

    <p>52 Mbp</p> Signup and view all the answers

    Which term describes genes that have diverged from a common ancestor?

    <p>Paralogues</p> Signup and view all the answers

    Which of the following is NOT an application of metagenomics?

    <p>Enhancing data extraction methods</p> Signup and view all the answers

    What is a potential purpose of pseudogenes in the genome?

    <p>To serve as a genetic reservoir for evolution</p> Signup and view all the answers

    Which gene is known as a phosphatase that removes phosphates from proteins?

    <p>PTEN</p> Signup and view all the answers

    What is a common feature of pseudogenes?

    <p>They resemble existing gene sequences but are non-functional</p> Signup and view all the answers

    What is one potential health implication associated with the human gut biome?

    <p>Disruptions in the gut biome can lead to worse cancer treatment outcomes</p> Signup and view all the answers

    Which chromosome contains the globin gene clusters mentioned?

    <p>Chromosome 11 and 16</p> Signup and view all the answers

    Which statement best describes orthologues?

    <p>Genes that perform the same function in different species</p> Signup and view all the answers

    What percentage of the human genome is made up of repeated sequences?

    <p>50%</p> Signup and view all the answers

    What is the estimated cost of the Earth BioGenome Project?

    <p>$4.7 billion</p> Signup and view all the answers

    Which pseudogene is recognized as a non-processed pseudogene?

    <p>HBBP1</p> Signup and view all the answers

    What can a genomic tree of life help to understand?

    <p>Processes of speciation, adaptation, and organism dependencies in ecosystems</p> Signup and view all the answers

    What defines a protein as hypothetical?

    <p>It is inferred from a genome sequence.</p> Signup and view all the answers

    What is the main role of post-translational modifications?

    <p>They add phosphates and sugars to proteins.</p> Signup and view all the answers

    What vitamin deficiency is highlighted as a major issue among children between ages 0-5?

    <p>Vitamin A deficiency</p> Signup and view all the answers

    What is Golden Rice genetically modified to contain?

    <p>Beta-carotene</p> Signup and view all the answers

    What has been the primary resistance to the introduction of Golden Rice in some countries?

    <p>Concerns over GMO seeds</p> Signup and view all the answers

    How many children become blind each year due to vitamin A deficiency?

    <p>250,000 to 500,000</p> Signup and view all the answers

    What type of modification has been specifically mentioned as an addition to the COVID-19 spike protein?

    <p>Glycosylation</p> Signup and view all the answers

    What does the addition of a phosphate by a kinase typically influence in proteins?

    <p>It modifies their behavior.</p> Signup and view all the answers

    What is the consequence of cells undergoing senescence?

    <p>They irreversibly withdraw from the cell cycle.</p> Signup and view all the answers

    Which of the following accurately describes Long-non-coding RNAs (lncRNAs)?

    <p>Long sequences greater than 200 nucleotides.</p> Signup and view all the answers

    How frequently do Single Nucleotide Polymorphisms (SNPs) occur in unrelated individuals?

    <p>Approximately 0.1% of sites.</p> Signup and view all the answers

    What privacy concern is raised by the use of consumer DNA sites by law enforcement?

    <p>Potential access to private genetic information without consent.</p> Signup and view all the answers

    What common feature do microRNAs possess?

    <p>They are approximately 22 nucleotides in length.</p> Signup and view all the answers

    What legal implication arose from the use of GEDmatch by law enforcement?

    <p>A judge approved a warrant to search the database.</p> Signup and view all the answers

    Which gene's involvement was critical in solving the 1984 murder case mentioned?

    <p>Thomas Garner.</p> Signup and view all the answers

    How many differences are estimated between any two unrelated individuals in terms of SNPs?

    <p>Approximately 30 million.</p> Signup and view all the answers

    What is the score when traversing left from a specific cell that contains a score of -4?

    <p>-6</p> Signup and view all the answers

    Which of the following directions is evaluated for scoring in this algorithm?

    <p>Left</p> Signup and view all the answers

    If a cell has a gap score of -2, what is inferred about the corresponding alignment?

    <p>An extended gap</p> Signup and view all the answers

    What is the score associated with a mismatch in this context?

    <p>-1</p> Signup and view all the answers

    What is the total score for the direction denoted by cell C 4 within the scoring matrix?

    <p>-8</p> Signup and view all the answers

    What is the score when traversing the LEFT direction from cell A1?

    <p>-4</p> Signup and view all the answers

    Which of the following scores would result from traversing vertically from cell A2?

    <p>-4</p> Signup and view all the answers

    What direction gives a score of 1 when starting from cell A0?

    <p>Vertical</p> Signup and view all the answers

    What is the gap score used when evaluating all directions from a starting cell?

    <p>-2</p> Signup and view all the answers

    What score would be obtained if traversing diagonally from cell A3?

    <p>-6</p> Signup and view all the answers

    What does the Needleman-Wunsch algorithm primarily accomplish?

    <p>Produces optimal global alignment</p> Signup and view all the answers

    What is a key feature of scoring matrices used in sequence alignment?

    <p>They help quantify similarity or identity between sequences.</p> Signup and view all the answers

    In the context of pairwise sequence algorithms, what is dynamic programming utilized for?

    <p>To build optimal alignments from smaller subsequences.</p> Signup and view all the answers

    How does the Smith-Waterman algorithm differ from the Needleman-Wunsch algorithm?

    <p>It focuses on local alignment.</p> Signup and view all the answers

    What is the purpose of including a gap penalty in alignment algorithms?

    <p>To account for insertions and deletions in sequences.</p> Signup and view all the answers

    Which method is used to trace back through an alignment score matrix in the Needleman-Wunsch algorithm?

    <p>Recursive traversal</p> Signup and view all the answers

    What type of scoring technique does an Identity Matrix use for aligning identical bases?

    <p>A score of 1 for matches and 0 otherwise</p> Signup and view all the answers

    What is a primary advantage of the BLOSUM matrices over PAM matrices?

    <p>They provide broader evolutionary coverage.</p> Signup and view all the answers

    What score is assigned when a match occurs during traversal of the algorithm?

    <p>1</p> Signup and view all the answers

    Which direction provides the maximum score during the evaluation process?

    <p>VERTICAL</p> Signup and view all the answers

    What should be kept to potentially produce the maximum value in the algorithm?

    <p>All arrows</p> Signup and view all the answers

    What is assigned to the cell for a mismatch during the traversal?

    <p>-1</p> Signup and view all the answers

    What happens to the score in a cell when the maximum value is reached?

    <p>It becomes the maximum value</p> Signup and view all the answers

    Which of the following scores indicates a gap in the evaluation?

    <p>-2</p> Signup and view all the answers

    During evaluation, scoring for cell values should prioritize which direction?

    <p>The direction yielding the best score</p> Signup and view all the answers

    What is the effect of selecting only the arrows that contribute to the maximum score?

    <p>Maximizes efficiency</p> Signup and view all the answers

    What value is assigned to the cell when traversing from diagonal to the next cell?

    <p>1</p> Signup and view all the answers

    What score does the cell contain if no valid path is discovered?

    <p>-4</p> Signup and view all the answers

    What is the time complexity of the basic Needleman-Wunsch algorithm?

    <p>O(n^2)</p> Signup and view all the answers

    Which modification of the Needleman-Wunsch algorithm is central to the Smith-Waterman algorithm?

    <p>Setting the initialization scores to zero</p> Signup and view all the answers

    What is the purpose of tracing back in the Smith-Waterman algorithm?

    <p>To find the maximum score path</p> Signup and view all the answers

    In the Smith-Waterman algorithm, what is done if F(i, j) is found to be less than a threshold t?

    <p>The value is replaced with zero</p> Signup and view all the answers

    Which of the following statements about the memory requirements of algorithms is true?

    <p>Memory requirements for the Needleman-Wunsch algorithm can be improved to O(n).</p> Signup and view all the answers

    What is the scoring method used in the Smith-Waterman algorithm for calculating F(i, j)?

    <p>max(F(i - 1, j - 1) + s(xi, yj), 0)</p> Signup and view all the answers

    What is the result of the FOPT calculation in the Smith-Waterman algorithm?

    <p>It finds the highest score in the matrix.</p> Signup and view all the answers

    Which of the following methods can be used to initiate a local alignment in the Smith-Waterman algorithm?

    <p>Starting at cells scoring above a threshold</p> Signup and view all the answers

    What is the correct syntax for defining an empty dictionary in Python?

    <p>dict = {}</p> Signup and view all the answers

    Which of the following correctly handles a situation when looking up a value that does not exist in a dictionary?

    <p>Using 'in' before accessing the dictionary will prevent a KeyError.</p> Signup and view all the answers

    Which types of objects are valid keys in a Python dictionary?

    <p>Strings and numbers</p> Signup and view all the answers

    What is the primary function of a dictionary in Python compared to a traditional array?

    <p>It retrieves values based on custom keys.</p> Signup and view all the answers

    What would happen if you try to look up a key that does not exist in a dictionary without handling it properly?

    <p>It will raise a KeyError.</p> Signup and view all the answers

    Which method is used to obtain a list of keys from a dictionary?

    <p>dict.keys()</p> Signup and view all the answers

    What syntax allows you to iterate through both keys and values in a dictionary?

    <p>for k, v in dict.items():</p> Signup and view all the answers

    What is the expected output of print(dict.items()) given a dictionary where keys are 'a', 'o', 'g'?

    <p>[('a', 'alpha'), ('o', 'omega'), ('g', 'gamma')]</p> Signup and view all the answers

    What is one recommended strategy for building a Python program effectively?

    <p>Identify and tackle milestones incrementally.</p> Signup and view all the answers

    What performance advantage does a dictionary provide in programming?

    <p>It organizes data through key-value pairs for quick access.</p> Signup and view all the answers

    What will be the result of trying to print the value of a key that does not exist in a dictionary?

    <p>It raises a KeyError.</p> Signup and view all the answers

    Which method can be used to safely access a value in a dictionary without raising an error if the key is not present?

    <p>dict.get(key)</p> Signup and view all the answers

    What happens if you try to delete a key that is not present in the dictionary using the del statement?

    <p>It raises a KeyError.</p> Signup and view all the answers

    How are keys stored in a Python dictionary when items are inserted?

    <p>They maintain the order of insertion.</p> Signup and view all the answers

    Which of the following statements about dictionaries is incorrect?

    <p>The order of items is not preserved.</p> Signup and view all the answers

    What method should be used to remove an item from a dictionary while avoiding exceptions?

    <p>Check for existence before using del or pop.</p> Signup and view all the answers

    When iterating over a dictionary, what is the default behavior concerning the elements accessed?

    <p>It iterates over the keys.</p> Signup and view all the answers

    What does the statement matrix[1,2] = 5 signify in the context of dictionaries?

    <p>Inserts key (1, 2) with value 5 into matrix.</p> Signup and view all the answers

    What does the function pick_a_codon return?

    <p>A codon based on a specific amino acid</p> Signup and view all the answers

    What does the variable 'stop_test' represent in the context of the code?

    <p>The position of the first stop codon detected</p> Signup and view all the answers

    What will happen if the count of codons is equal to two in the select_random calculation?

    <p>It will select between 0 and 1</p> Signup and view all the answers

    Which statement is true about seq1 in the code?

    <p>seq1 is not an open reading frame.</p> Signup and view all the answers

    What is the purpose of the print statement after checking seq1?

    <p>To indicate whether seq1 contains a stop codon</p> Signup and view all the answers

    How is the codon_list created in the pick_a_codon function?

    <p>By matching amino acids with their corresponding codons</p> Signup and view all the answers

    What should be modified in the approach to selecting a new codon from the codon_list?

    <p>Use select_random without adjusting for the index</p> Signup and view all the answers

    What is the role of the make_aminos function indicated in the sample code?

    <p>To create a dictionary of amino acids</p> Signup and view all the answers

    What is the purpose of the 'make_aminos' function in the provided code?

    <p>To create a dictionary mapping codons to amino acids.</p> Signup and view all the answers

    In Part 2 of the process, what is primarily stored in the 'protein1' string?

    <p>The growing sequence of amino acids translated from seq1.</p> Signup and view all the answers

    What programming structure is suggested for pulling codons from seq1?

    <p>A while loop that pulls three nucleotides at a time.</p> Signup and view all the answers

    When developing the dictionary to be used in the program, which of the following is NOT a characteristic of the entries?

    <p>A codon can correspond to multiple amino acids.</p> Signup and view all the answers

    How is the 'new_seq1' string expected to be modified during the translation process?

    <p>It accumulates new codons based on the translated amino acid sequence.</p> Signup and view all the answers

    What type of data structure is used to store the codon-to-amino acid mappings?

    <p>A dictionary.</p> Signup and view all the answers

    Which sequence is confirmed to be composed of multiples of 3 for processing?

    <p>seq1.</p> Signup and view all the answers

    What should the initial value of the loop variable be to start translating seq1?

    <ol start="0"> <li></li> </ol> Signup and view all the answers

    Study Notes

    Genome Browsers

    • UCSC, NCBI, and Ensembl are the “Big 3” genome browsers
    • NCBI includes ClinVar, a database with publicly submitted variations, and dbSNP, a database of SNPs
    • GnomAD is a genome aggregation database and also a good source for variant information

    UCSC

    • UCSC Genome Browser is available at http://genome.ucsc.edu/
    • UCSC provides the Track View and Table Browser
    • UCSC offers two assemblies: GRCh38 and GRCh37 with different levels of annotation
    • GRCh38 has fewer gaps and is newer, while GRCh37 is older and has more annotations

    NCBI

    • NCBI is available at https://www.ncbi.nlm.nih.gov/
    • NCBI focuses on database queries.
    • ClinVar displays submitted variations and observed disease associations
    • dbSNP (a database of SNPs) is also housed within NCBI
    • GEO (Gene Expression Omnibus) offers over 100,000 expression experiments
    • PubMed lists publications

    Ensembl

    Gnomad

    • Gnomad is available at https://gnomad.broadinstitute.org/
    • Provides information on position, change, minor allele frequency (MAF), consequence, and clinical significance
    • Gnomad is frequently updated, so the content in screenshots may not always be the same.

    UCSC Anatomy

    • Coordinates can be entered by gene symbol or coordinates
    • Track View displays various data types
    • You can zoom in/out and pan left/right
    • You can access DNA view and analyze at the amino acid level
    • The strand direction reveals if the gene is on the reverse (3’ to 5’) strand

    UCSC Tracks

    • The Track View is organized by type, such as mapping, genes, phenotype, etc.
    • Users can turn on/off different tracks of data
    • Tracks provide links to additional information

    NCBI

    • NCBI's data extraction tools are complicated

    Ensembl Automation

    • Ensembl provides automated extraction tools
    • It offers a Perl API for programmatic data extraction and a REST (representational state transfer) interface that supports Perl, Python, Java, and other languages

    Proteomics

    • Proteins need to be experimentally verified to exist and for their properties to be measured
    • Post-translational modifications change protein behavior from what the genetic sequence alone indicates
    • Addition of a phosphate by a kinase is a post-translational modification
    • Addition of sugar to a protein is a post-translational modification, like in the COVID-19 spike protein

    Vitamin A Deficiency

    • 250,000 to 500,000 children become blind every year due to vitamin A deficiency
    • Data on vitamin A deficiency worldwide collected from 1991 to 2013

    Golden Rice

    • Genetically modified to contain beta-carotene, a precursor to vitamin A
    • Anti-GMO groups fought against the introduction of golden rice in Bangladesh

    Concerns about GMOs

    • A 2017 review found no evidence that GMO animal feed has adverse effects on animal health
    • Trillions of animals have been fed with GMO feed without negative health consequences
    • Switching to non-GMO feed has negative consequences
      • Increases greenhouse gas emissions by 7%
      • Increases land use
      • Raises food prices

    Mutation Breeding

    • Modern agriculture has practiced mutation breeding for the last 100 years
    • Chemicals or radiation are used to increase mutations, resulting in new varieties
    • This process is not considered GMO
    • A 2017 PNAS report found no evidence that foods from GE crops are less safe than foods from non-GE crops

    Earth BioGenome Project

    • Proposed to sequence the genomes of all named extant eukaryotes, about 2 million species
    • Aims to create a digital library of life on earth
    • Projected to cost $4.7 billion

    Metagenomics

    • Analysis of all the genomics in a coherent environmental sample
    • Examples of environments studied: 1 ml of ocean water, 1 gram of soil, and human gut

    Applications of Metagenomics

    • Studies human gut biome and its relation to health
    • Applies to agriculture, environmental remediation, anthropology, and biotech

    Gene Terminology

    • Paralogues are genes that diverged from a common ancestor
    • Orthologues are genes that perform the same function in different species

    Pseudogenes

    • Are typically non-functional genes
    • Appear like existing gene sequences
    • Likely arise from DNA duplication or retro-transposition

    Pseudogene.org

    • Comprehensive database and comparison platform for pseudogene annotation
    • Estimates approximately 10,668 processed pseudogenes and 14,000 non-processed pseudogenes

    PTEN: Phosphatase and Tensin Homolog

    • Is a phosphatase, which removes phosphates from a protein

    Gene Names

    • Ambiguous, have aliases, synonyms, and historical names
    • Example: Hemoglobin Subunit Gamma 1

    Globin Gene Clusters

    • Located on chromosomes 16 and 11

    Human Genome

    • Contains 3.2 * 109 nucleotides (haploid)
    • Chromosome sizes range from 49 Mbp to 279 Mbp
    • Repeated sequences make up 50% of the genome

    Cell Senescence

    • Can result from the normal shortening of telomeric DNA
    • Cells irreversibly withdraw from the cell cycle and fail to respond to proliferation-inducing stimuli

    RNA

    • Thousands of transcripts (alternatively spliced) in a human genome
    • LncRNAs: Long-non-coding RNAs (length > 200 nucleotides)
    • MicroRNAs: ~22 nucleotides in length whose function is RNA silencing

    SNPs

    • Single Nucleotide Polymorphisms
    • Compare any 2 un-related individuals, they will be different at approximately 0.1% of sites (1 in 1,000).
    • 3109 * 0.001 = 3107 = 30,000,000 differences

    Privacy Concerns

    • 20 million people have uploaded their genetic profiles to consumer DNA sites
    • Concerns that police can access this genetic data to solve crimes
    • First case in which a judge approved a warrant to penetrate GEDmatch and search its database

    Case Example

    • A Florida jury found Thomas Garner guilty of first-degree murder for the 1984 death of Navy recruit Pamela Cahanes using genetic data

    Atomic Level Interactions

    • DNA binding is a significant process at the atomic level.

    Cross-Species Genome Similarity

    • "Islands of Similarity" indicate areas of shared genetic material between different species.

    Scoring Matrices

    • Identity matrices assign a score of 1 for identical characters and 0 for non-identical ones.
    • Similarity matrices consider the similarity between characters, allowing for scores that reflect the evolutionary relationship between them.
    • PAM and BLOSUM matrices are examples of commonly used scoring matrices.

    Pairwise Sequence Algorithms

    • Optimal alignments can be constructed based on previous solutions for smaller subsequences.
    • Dynamic programming is used to optimize the process, by calculating the best alignment that ends at a given pair of positions (i,j).

    Key Elements of Sequence Alignment Algorithms

    • Global pairwise alignment aims to align the entire length of two sequences, while local alignment identifies the best possible local alignment within the sequences.

    Needleman-Wunsch Algorithm

    • This algorithm produces an optimal global alignment between two sequences.
    • It uses a 2D matrix to store partial alignment scores and iteratively calculates the best alignment.
    • Scoring functions are used to assign values to matches, mismatches, and gaps.
    • The actual alignment is constructed during the traceback phase of the algorithm, starting from the cell with the highest score and tracing back to the beginning.

    Smith-Waterman Algorithm

    • This algorithm focuses on local alignments, seeking the most significant region of similarity within two sequences.
    • It modifies the Needleman-Wunsch algorithm to account for local alignment by setting negative scores to 0.
    • The traceback process starts at the highest-scoring cell and ends when 0 is encountered.
    • The algorithm can also be used to identify all local alignments that exceed a designated threshold.

    Computational Complexity of Needleman-Wunsch Algorithm

    • The algorithm has a computational complexity of O(n^2) for both speed and memory.
    • Advanced versions can reduce memory usage to O(n), achieving linear space complexity.

    Global vs. Local Alignment

    • Global alignment seeks to align the entire lengths of two sequences.
    • Local alignment identifies the best possible local region of similarity within two sequences.

    Smith-Waterman Algorithm

    • The initialization step sets the scores for the first row and column of the matrix to 0.
    • The iteration step computes the score of each cell based on the maximum value obtained from three possible directions: alignment with a gap in the first sequence, alignment with a gap in the second sequence, or aligning the current characters.
    • The termination and traceback phase involves identifying the cell with the highest overall score and tracing back to the starting point to reconstruct the optimal alignment.

    Homework Assignment

    • Students are required to complete a matrix for the Needleman-Wunsch algorithm and recover the corresponding alignment.
    • They also need to create a "B" matrix in Python.

    Recursion Example - Fibonacci Sequence

    • The Fibonacci sequence is a numerical series where each number is the sum of the two preceding numbers.
    • The sequence starts with 0 and 1.
    • To find the Fibonacci sequence:
      • Add the last two digits to get the next digit.
      • Repeat the process to generate the remaining digits.

    Dictionary Hash Tables

    • Python's dict is a hash table data structure that efficiently stores key-value pairs.
    • Dicts are created by using curly braces {} and are written as a series of key:value pairs, e.g., dict = {key1:value1, key2:value2, ...}.
    • An empty dict is represented by an empty pair of curly braces {}.

    Dict Access Operations

    • Accessing or setting a value within a dict uses square brackets:
      • dict['foo'] looks up the value associated with the key 'foo'.
      • dict['foo'] = bar assigns the value bar to the key 'foo'.
    • Keys in dicts can be strings, numbers, and tuples.
    • Values can be of any data type.
    • Attempting to access a non-existent key raises a KeyError.
    • Use the in operator to check if a key exists: 'foo' in dict.
    • The dict.get(key) method returns the value associated with the key, or None if the key is not present.
    • The dict.get(key, not-found) method allows specifying a default value to return if the key is not found.

    Example of Building a Dict

    • A dict can be built incrementally by starting with an empty dict {} and adding key-value pairs using the assignment operator:
      • dict['a'] = 'alpha'
      • dict['g'] = 'gamma'
      • dict['o'] = 'omega'

    Using Dictionaries as N-dimensional Arrays

    • Dictionaries can function like N-dimensional arrays, storing values associated with multi-dimensional keys.
    • The keys can be tuples or other composite data structures.
    • Example: matrix[1, 2] = 5 assigns the value 5 to the key (1, 2).

    Dict Iteration and Ordering

    • By default, iterating over a dictionary (for key in dict: ...) iterates through its keys in an arbitrary order.
    • Key-value pairs in a dictionary maintain the order in which they were originally inserted.
    • dict.keys() returns a list of the keys.
    • dict.values() returns a list of the values.
    • dict.items() returns a list of (key, value) tuples, providing the most efficient way to access all the key-value data.
    • These list methods' output can be sorted using the sorted() function.

    Performance Advantages of Dicts

    • Dictionaries provide a significant performance advantage for looking up and managing data based on keys.
    • Utilize dictionaries when possible to organize and access data efficiently.

    Incremental Development (Rapid Prototyping) in Python

    • Don't write entire Python programs at once.
    • Identify smaller milestones and write code to reach them one at a time.
    • Use print statements to inspect data structures at each milestone.
    • Use sys.exit(0) to halt program execution after a milestone to focus on specific areas.
    • This gradual approach allows for quick testing and iteration, making it easier to build and refine complex programs.

    Introduction to Lab 4 - Creating a Dictionary of Codons and Amino Acids

    • The lab focuses on building a dictionary representing the mapping between codons (three-nucleotide sequences) and their corresponding amino acids.
    • You will complete a dictionary (aminos) containing this information.
    • The lab provides code to translate DNA sequences into amino acid sequences using the aminos dictionary.

    Lab 4 Key Concepts:

    • The code includes a function pick_a_codonthat randomly selects a codon for a given amino acid (if there are multiple codons that map to the same amino acid).
    • The lab emphasizes understanding the structure and manipulation of dictionaries in Python for tasks like translation (DNA -> Amino Acid).
    • It also introduces concepts like open reading frames (sequences that are translated into proteins until a stop codon is encountered).

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    Related Documents

    Panorama Of Life - Introduction PDF
    Panorama of Life Chapter 3 PDF
    Alignments and Phylogenetic Trees PDF
    Python Dicts and Files PDF

    Description

    Test your knowledge on the major genome browsers: UCSC, NCBI, and Ensembl. Learn about their features, databases, and offerings, including ClinVar and dbSNP. This quiz covers essential details that every genomics enthusiast should know.

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