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Genetics - Distance Matrix

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Using the table below, build a genetic distance matrix which gives the total number of genetic differences between pairs of unique haplotypes in the sample. The first box is filled in for you, by way of an example.

Haplotypes 1 2 3 4 5
1 -- 2
2 --
3 --
4 --
5 --

Complete the phylogenetic tree below which places the chimpanzee as the ancestral outgroup for the collection of human haplotypes. To do this, label the ends of the branches with the haplotype designations (Haplotype 3 has already been added, by way of an example) and label the lengths of the branches with the names of the SNPs whose alleles mutate as the haplotypes evolve (SNP6 has changed, for example, between the chimpanzee outgroup and Haplotype 3). Hint: use the results of part (h) to help guide your decision-making.

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Solution Summary

Completing a phylogenetic tree based on a distance matrix.

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Genetics: Exons, Sequencing, and Bioinformatics

Multiple Choice Practice Problems

1) Exon prediction procedures (EX: hexmar frequency) works best in predicting which of the following exons?
(A) 3' exons
(B) 5' exons
(C) Internal coding exons
(D) Internal non-coding exons

2) Which of the following scoring matrices would work best for searching for divergent sequence homologs using BLAST?
(C) PAM120
(D) PAM160

3) Which of the following statements correctly describes the "FIRST STEP" of BLAST heuristic?
(A) Extend hits to differentiate random hits from meaningful hits
(B) Search database using Boyer-moore string matching algorithm
(C) Use dynamic programming to align the query sequence to database sequences
(D) Compile a list of high scoring words from the query sequence

4) Which of the following statements about Smith-waterman sequence alignment methods is correct?
(A) Traceback continues until a cell with a score of zero is reached
(B) Traceback begins at the minimum scoring element in the matrix
(C) The Smith-waterman method generates global sequence alignment
(D) The smith-waterman method does not include gap penalties

5) Which of the following statements about PSI-BLAST method is correct?
(A) PSI-BLAST uses CLUSTALW to construct a sequence alignment of the HSPs
(B) PSI-BLAST is more sensitive than gapped BLAST to detect weak sequence homologs
(C) PSI-BLAST can only be run for a single iteration
(D) PSI-BLAST searches the sequence database using the Smith-waterman algorithm
(E) All of the above

6) Which of the following statements best describes an advantage of using flat text file bioinformatics database?
(A) Text file database supports multiple users to read or write to the database concurrently
(B) Text file database enforces the integrity and consistency of data in the database
(C) Text files enable database transactions to be rolled back if the computer crashes
(D) Text file database facilitates data exchange

7) Which of the following statements correctly describes an advantage of building an index for a database table?
(A) An index increases the speed and efficiency of a search or query
(B) An index enables a database transaction to be rolled back if the computer crashes
(C) An index allows multiple users to read or write to the database
(D) An index reduces the disk space required to store the data in the table

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