Homology vs Similarity

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Questions and Answers

Match the terms with their correct definitions in the context of sequence alignment:

Homology = Similarity due to shared ancestry. Percent Identity = The extent to which two sequences are identical. E-value = The expected number of alignments with a score as good as or better than the observed alignment that would occur by chance. P-value = The probability of obtaining an alignment score as good as or better than the observed alignment by chance.

Match the statistical measures used in sequence alignment with their descriptions:

P-value = The probability that at least one sequence will produce the same score by chance. E-value = The expected number of sequences that will produce the same or better score by chance. Z-score = Measures how many standard deviations above the mean the score distribution is. Homology = Similarity due to shared ancestry.

Match the concepts with their descriptions relevant to sequence alignment:

Scoring Matrix = A system of assigning scores for matches and mismatches in sequence alignment. Statistical Significance = A measure to determine if a result is likely due to chance. Homology = Inference about shared ancestry based on sequence similarity. Functional Identification = Determining the role of a gene or protein based on sequence similarity to known sequences.

Match the steps in calculating the statistical significance of sequence alignments with their related concepts:

Expected Number of Matches = Calculating the number of matches based on sequence length and probability. Statistical Significance = Providing a universal measure for inferring homology. Karlin-Altschul Statistics = Significance of local alignments without gaps. Similarity = Quantifying how similar sequences have to be to infer homology. Signup and view all the answers

Match the terms with their descriptions in the process of assessing similarity between biological sequences:

Homology = Inference of a common evolutionary ancestor based on significant similarity. Percent Identity = Percentage of identical positions between two aligned sequences. Scoring Matrices = Tables of values that determine the score of aligning each possible pair of residues. Statistical Significance = Assessment of whether the similarity observed is higher than what would be expected by chance. Signup and view all the answers

Match alignment concepts with their descriptions:

Homology = Similarity resulting from common ancestry. Percent Identity = Measure of the percentage of identical positions in an alignment. Statistical Significance = Method for determining whether an alignment is likely due to chance or a real biological relationship. Scoring Matrix = Table that assigns values to matches and mismatches. Signup and view all the answers

Match the statistical aspects of sequence analysis to their significance:

P-value = Indicates the probability that random chance could produce an alignment with a score as good as or better than the actual alignment. E-value = Estimates the number of alignments expected by chance with scores equal to or better than that of the actual alignment. Scoring matrices = May assign different scores for matching different amino acids. Percent Identity = May present problems when sequences are distantly related. Signup and view all the answers

Match the terms to their corresponding descriptions in the analysis of sequence similarity:

BLOSUM = A matrix used in sequence alignment to score the similarity between amino acids. PAM matrix = A matrix developed to model protein evolution and calculate the likelihood of amino acid substitutions. Homology = Shared ancestry inferred from sequence similarity. Percent Identity = Extent to which two sequences align exactly. Signup and view all the answers

Match the terms with their descriptions related to statistical measures in sequence alignment:

E-Value = The number of expected hits of similar quality (score) that could be found just by chance. P-Value = The probability of observing a score as extreme as, or more extreme than, the score assuming the null hypothesis is true. Z-score = Quantifies how many standard deviations from the mean a particular data point is. Alignment Score = Reflects the sum of scores for aligned pairs of residues. Signup and view all the answers

Match the concepts of sequence alignment with their relevant descriptions:

Homology = Similarity shared due to common ancestry. Sequence alignment = Arranging sequences to identify regions of similarity. Statistical significance = Determines the likelihood that the alignment occurred by chance. Scoring matrices = Assigns values to matches and mismatches. Signup and view all the answers

Match the terms with their correct association in sequence alignment analysis:

E-value = The likelihood that similar matches might occur by random chance. P-value = The probability that random chance alone could produce the observed alignment or a better one. Statistical Significance = Assessing whether an alignment is likely due to chance or a genuine relationship. Sequence Similarity = The degree to which two sequences are alike. Signup and view all the answers

Match the sequence alignment concepts with their appropriate descriptions:

Sequence Similarity = The degree of resemblance between two or more sequences. Homology = Evolutionary relationship inferred from sequence similarity. Scoring Matrix = A system of assigning scores for matches, mismatches, and gaps in alignments. Statistical significance = Measures the reliability of sequence alignments. Signup and view all the answers

Match the following terms to their roles in sequence analysis:

BLAST = A tool used for comparing a query sequence against a database of sequences. FASTA = An algorithm used for local sequence alignment. E-value = Assessment of statistical significance. Scoring matrix = Values assigned for matches or mismatches. Signup and view all the answers

Match the bioinformatics terms with their most accurate descriptions:

BLAST = A sequence alignment algorithm used to compare primary biological sequence information. FASTA Statistics = Estimates the probability distribution of alignments for every query. Scoring Matrix = Assign values to matches and mismatches in sequence alignments. Percent Identity: = How much similarity needed to rely on results. Signup and view all the answers

Match the terms with their descriptions in sequence alignment and statistics:

E-value = The expected number of sequences with scores equal to or better than the observed score. Statistical significance = Estimation of whether an alignment is real or due to chance. Sequence Alignment = Identifying regions of similarity that may be a consequence of functional, structural, or evolutionary relationships. Homology = Similarity in sequence resulting from shared ancestry. Signup and view all the answers

Match the statistical measures to their respective applications in sequence alignment analysis:

E-value = Quantifies the likelihood that the similarity between two segments is due to random chance alone. P-value = The probability of finding the current, or a more significant, alignment by chance alone assuming no relationship between the sequences. Homology = Common ancestry, inferred from similarity. Sequence Similarity = Measures the degrees to which two sequence are alike. Signup and view all the answers

Match the sequence comparison terms with the phrases that describe them

Sequence Alignment = Arranging sequences to highlight similarity. P-value = Describes alignment due to random relationships. E-value = The expected number of sequences with scores equal to or better than the observed score. Homology = Similarity in sequence resulting from shared ancestry. Signup and view all the answers

Associate the sequence alignment algorithms with their most distinguishing features or applications:

BLAST = Fast database searching for sequence homology. FASTA = Sequence alignment algorithm used for sequence comparison. Local Alignment = Finding regions of similarity between sequences. Global Alignment = Aligning the entire length of two sequences for maximum similarity. Signup and view all the answers

Match each term with its appropriate application or meaning in the context of sequence analysis:

Homology = Relationships inferred from sequence similarly. P-value = Assesses whether alignment is likely due to chance or biological relevance. Scoring matrix = Values assigned for matches or mismatches during sequence alignment. BLAST = Algorithm used for local sequence alignment. Signup and view all the answers

Match the descriptions with the measures of similarity:

Percent identity = The portion of two sequences are have an exact match. Scoring matrices = Assigned different values for match different amino acids. Statistical significance = Goal is to provide a universal measure for inferring homology. P-value = The probability the at least one sequence will produce the same score by chance. Signup and view all the answers

Match the statistical measures tools with their descriptions:

Erdös-Rényi = Describes significance of a match-run. Karlin-Altschul statistics = Describes significance of local alignments without matches. Scoring matrices = Description for statistics for local alignments without gaps. Statistical significance = Description for providing a universal measure for inferring homology. Signup and view all the answers

Match each term with its description:

Local alignment = Identify conserved regions. Global alignment = Over entire length of query sequences. Statistical Significance = Measures the reliability of sequence alignments. Homology = Similarity resulting from common ancestry. Signup and view all the answers

With respects to scoring matrices, please match the following:

Log odds ratio = Dayhoff way of representing similarity of a.a. q_ij = The observed frequency of co-occurrence. BLOSUM = a matrix that is an alternative to the PAM. λ (lambda) = Close related to the matrix used in constructing scoring matrixes. Signup and view all the answers

Match the sequence alignment distribution with its definition

Extreme Value Distribution = A guimble distribution. Guimble distribution = The resulting alignments values from the most well aligned random strings and query. Normal Distribution = Description for some of the alignments. Statistical significance = The overall goal. Signup and view all the answers

Match the sequence types with their probability:

DNA Sequence = Base composition (uniform) and no gaps, but it's a good estimate. Coin Tosses = The tricky method of modeling amino acid sequence alignments. Matching Runs = The head-run problem of coin tosses Sequence Alignment Similarity = 40% similar, 70% similar Signup and view all the answers

Match the coins tosses analysis with their descriptions

R=log1/p(n) = The length of the longest run of heads p = the probability of a head = Coin toss probability. E(s>=x) = The expected number of matching runs with a score x or higher. E(l) = np^1 = The expected number of a length 1 run of heads. Signup and view all the answers

Match each term that refers to BLAST with their discription

Raw Score = Converted to a bit score. E(sss 2-Sbit) = Computes the E value λ and K = Pre-computed for different scoring matrices. BLAST Allows = Only a certain range of gap penalties. Signup and view all the answers

Match the definitions of statistical analysis and sequence

Extreme Value Distribution = Consider an experiment that obtains the maximum value of locally aligning a result string, repeats the sequence to find the mean. Extreme Cluster Analysis = If one has a lot of weights on each cluster, it can be compared against a different sized cluster P(x ≥ w) = e-Akw = After we fit an exponential distribution, we compute the probability that another random cluster gets a higher score than the score of found cluster. Trick = Modeling dna (or amino acid) sequence alignments as coin tosses. Signup and view all the answers

Flashcards

Function Identification

Finding genes with similar functions across different organisms.

Homology

Similarity due to shared ancestry.