Biochemistry
9th Edition
ISBN: 9781319114671
Author: Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher: W. H. Freeman
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Chapter 6, Problem 15P
Interpretation Introduction
Interpretation:
A method to determine the most appropriate gap penalty should be suggested.
Concept introduction:
Gap penalty is a scoring method used in sequential alignment of two or more sequences. Introducing gaps to sequences will match more
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- why is gap opening penalized more than gap extension in doing alignment of sequence similarity?arrow_forwarda - What is Position-Specific Scoring Matrices (PSSM) and how do we obtain it? b - Construct the HMM for the following sequences where the matches are considered for the columns that don't have any gap T G A C А G T G A А G G T G G A G G C A G EE E E Earrow_forwardDiscuss why it is useful to search a database to identify sequencesthat are homologous to a newly determined sequence.arrow_forward
- Assuming that the mean size of the human sau3AI partially digested fragments clones is 3kb, calculate the proportion of the human genome represented in all libraries prepared by the class. Use a value of 3,000,000kb for the size of the human genome. You also need to know that the whole 'class' generated 3,514 white colonies on plate 2.arrow_forwardWhat possible errors can a BLAST search make when assessing gene function to determine practical and evolutionary associations?arrow_forwardwhich substitution matrix would you choose for a BLASTP search? justify your choice.arrow_forward
- Consider three different kinds of human libraries: agenomic library, a brain cDNA library, and a livercDNA library.a. Suppose that all three of these libraries are sufficiently large so as to represent all of the differenthuman nucleotide sequences that the library couldpossibly include. Which of these libraries wouldthen correspond to the largest fraction of the totalhuman genome?b. Would you expect any of these libraries not tooverlap the others at all in terms of the sequences itcontains? Explain.c. How do these three libraries differ in terms of thestarting material for constructing the clones in thelibrary?d. Why would you need to sequence many clonesfrom many cDNA libraries to annotate a genome?arrow_forwardRecall that constructs used for floxing a gene contain,within one of the gene’s introns, two loxP sites flanking a gene for neomycin resistance (Fig. 18.11a). AloxP site is only 34 base pairs long, as shown in thefollowing figure.ATAACTTCGTATA ATGTATGC TATACGAAGTTATInverted repeat Spacer Inverted repeatExplain how you could use PCR to generate a neomycin resistance gene flanked by loxP sites, starting witha plasmid containing a neorgene. If you had the intronof the target gene cloned in a plasmid vector, howcould you insert your PCR product into the intron?arrow_forwardCalculate the dynamic programming matrix and the optimal local and global alignment for the DNA sequences a: GAATTC and b: GATTA, scoring +2 for a match, -1 for a mismatch, and using a linear gap penalty function WL) = -2L thank youarrow_forward
- Hidden Markov Model (HMM) Construct the HMM for the following sequences 2) G C A A A A G A A T G C A A G A The matches are considered for the columns [1, 2,4,5, and 7]arrow_forwardTo determine the reproducibility of mutation fre-quency measurements, you do the following experiment.You inoculate each of 10 cultures with a single E. coli bac-terium, allow the cultures to grow until each contains 106cells, and then measure the number of cells in each culturethat carry a mutation in your gene of interest. You were sosurprised by the initial results that you repeated the experi-ment to confirm them. Both sets of results display the sameextreme variability, as shown in Table Q5–1. Assuming thatthe rate of mutation is constant, why do you suppose thereis so much variation in the frequencies of mutant cells indifferent cultures?arrow_forwardList down and briefly describe three other sequence alignment tools other than BLAST used in Bioinformatics.arrow_forward
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