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21 Aug 2018

what can we say about the alignment of Asp with Glu in two sequences when considering the BLOSUM 62 substitution matrix with respect to alignment by chance? help me please urgent

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Reid WolffLv2

23 Aug 2018

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Can anyone help me answer these in detail please. These are part of material i need to know for my next exam and have no clue about them and cant find anuthing in our lecture notes about them

1. Clonal sequencing methods vs. Shotgun sequencing methods. What are the differences, pros and cons of each?

2. Local vs. Global alignment. Understand the theory of the alignment methods that underlie these types of alignment and be familiar with NeedlemanâWunsch and Smith-Waterman.

3. Identify a strand based on the frame (+/-) and what a six-frame translation means

4. What types of sequences are the majority found in GenBank

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1. Hexokinase I has two domains each with a site that can bind glucose-6-phosphate inhibitor with equal affinity. However, the enzyme can bind only one molecule of glucose-6-phosphate at a time. What does it tell us about the effect of glucose-6-phosphate on the enzyme?

2. Glucose-6-phosphate is a competitive inhibitor of hexokinase I in respect of ATP but
a non-competitive inhibitor in respect of glucose. What does it tell us about the binding and physiological function of glucose-6-phosphate?

3. (2%) Indicate which secondary structure or structures (Î± -helix, Î² -pleated, random coil) will the following peptide adopt in an aqueous solution at pH 7 Gly-Pro-Glu-Ser-Ala-Tyr-Lys-Thr-Leu-Phe-Asp-Val-Pro-Asp-Asp-Glu-Asp-Gly-Gly

maroonreindeer451

Section A â Edit distance (8 points total)

1. Find the edit distance between ACGAAGTTC and ACCAAGGTGTTC. How do you know it is at most that much? How do you know it is at least that much?

Section B â More on sequence alignment (52 points total)

2. (6 points) Which of the following would be the two most appropriate to assess whether there are regions of homology between two distantly related proteins? Select two.

A) Needleman-Wunsch Algorithm

B) edit distance

C) local sequence alignment

D) global sequence alignment

E) dot plot

3. Consider the following alignment: ACACCAGGTCCCC ACA-----TGACC

a) (3 points) With a match score of +3, and mismatch score of -1, and using a gap penalty of -2, what is the score of the above alignment?

b) (3 points) If we keep the same match score and mismatch score, but use a gap open penalty of -6 and a gap length penalty of -1 per additional residue, what is the score of the previous alignment?

c) (8 points) Using the scoring system used in part b (match +3; mismatch -1; gap open -6 ; gap extension -1), Which of the following alignments is best? Which is worst? How do you know?

A) ACACCAGGTCCC A---CATGA-CC

B) ACACCAGGTCCC ACA---TGACC

C) ACACCAGGTCCC ACATGA----CC

D) ACACCAGGTC-CC ACA-----TGACC

E) ACACCAGGTCCC ACA--TG-ACC

F) ACA---CCAGGTCCC ACATGACC-------

4. Look up the INS gene in Entrez Gene.

a) (2 points) What tag do you put inside square brackets after INS to search for INS as a gene symbol?

b) (2 points) Find the record for the human INS gene. Which chromosome is INS on?

c) (2 points) What is the accession number for the RefSeq record for the shortest mRNA for human INS?

d) (2 points) What is the accession number for the RefSeq record for the human geneâs genomic DNA?

d) (6 points) Using the Needleman-Wunsch program, how could you find the mRNA sequence within the genomic DNA version? Give the best strategy, including the scoring parameters.

e) (4 points) Find the next gene upstream of the INS transcription start site. Which neurotransmitter does the product of this next gene make? How many base pairs separate the two genes?

f) (2 points) Now look up ins-1 as a gene symbol in Entrez Gene. Choose the entry for the worm C. elegans. Which chromosome is it on?

g) (2 points) What is the URL for the Wormbase link on this Entrez Gene record? What is the gene accession number for ins-1 in the C. elegans genome database?

g) (10 points) Perform Needleman-Wunsch alignments between C. elegans INS- 1 protein and Homo sapiens INS preproprotein, using the default parameters, except changing the substitution matrix to PAM10 for one alignment, and PAM50 for the second alignment. Use the following online tool: https://www.ebi.ac.uk/Tools/psa/emboss_needle/ What are the number of identical residues, score, and number of gapped residues for each of the two alignments? What conclusions can you draw about which of the two matrices, PAM10 or PAM50, is more appropriate in this situation?