Biochemistry (Looseleaf)
9th Edition
ISBN: 9781319114800
Author: BERG
Publisher: MAC HIGHER
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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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Based on the question,give an asnwer Question : Name the scoring matrix “A”. List the advantage(s) of this scoring matrix.
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- please help asap! thanksarrow_forwardwhy is gap opening penalized more than gap extension in doing alignment of sequence similarity?arrow_forwardUsing the Dynamic Programming algorithm for pairwise local alignment we covered in class, construct the dynamic programming score table for a local alignment of the following two sequences, using the following scoring parameters: match score = +5, mismatch score = -3, gap penalty = -2.: ACGTATCGCGTATA GATGCTCTCGGAAAWhat is score of the best local alignment between these two sequences? Show the alignment of these sequences. asaparrow_forward
- The SCAM data for positions V51C and Y96C are different to the other datasets. Describe how the data for these positions are different to the other positions. In each case, explain what the structural basis of these differences may be.arrow_forwardConsider 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_forwardHow are the gap penalties adjusted in the ClustalW multiple sequence alignment program to improve the algorithm? Indicate the logic only.arrow_forward
- asap pleasearrow_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_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_forward
- Why the sequence alignment is extremely important in designing a construct for developing a transgenic plant, explain it?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_forwardalignment in genomic research, list types of alignments and corresponding errors associated with specific sequence assemblies. Are there methods of alignment error filtering?arrow_forward
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