Bioinformatics Answers

What connects upper limbs and vertical column

Outline the steps used to find values for a BLOSUM amino acid similarity matrix.

What are different nucleotide and protein databases? Describe the salient features of each with emphasis on pros and cons. 

A scientist sequencing mRNA identifies the following strand: CUAUGUGUCGUAACAGCCGAUGACCCG What is the sequence of the amino acid chain this mRNA makes when it is translated?

A scientist wants to clone a molecule bearing UniProtKB accession number P43657. How will he come to

know about the following?

I. Exact genomic location of the molecule under investigation

II. Coding and noncoding segments of the molecule

III. Untranslated regions of the molecule

A scientist sequencing mRNA identifies the following strand:

CUAUGUGUCGUAACAGCCGAUGACCCG 

What is the sequence of the amino acid chain this mRNA makes when it is translated?

pattern and profile used in the sequence analysis for functional assignment

Here are two motifs. Which of the following matches them?

[QAPRG]-X-D-Q-X-{RT}-X-S

A. QQQQQQQS

B. PPDQDDDS

C. LLDQQLLS

D. QQDQQTQS

E. GGDQGGGS

G-[AWEE]-X- X-{EGR}-X-{WE}

A. GGEPRGP

B. GAAAAGG

C. GWEPAGG

D. GWEPAGP

E. GREETLP

Part B. PDB Files. 5 Marks

1. Go to the PDB home page,

http://www.rcsb.org/pdb/ . Retrieve the 3NSJ file. What is the

protein that is the subject of this file, and from what species?

2. Why do you think the authors wanted to determine the structure of this protein?

3. Describe some of the insights into the function of the protein the structure gave.

4. What experimental technique was used to collect the data? What is the resolution of the

derived structure (in angstroms)

5. Approximately how many alpha helices and beta sheets does the protein contain?

1. For the sequence below, answer the following questions.

a) Identify the protein and species

b) At approximately what amino acid number is the most hydrophilic region

of the protein?

Use the default window size for the tool you use.

You

must state which tool/program you have chosen to use.

c) Do you expect it to be secreted? If so, by what mechanism?

d) List the motifs that are identified. Use the standard parameters for the tool

you choose to use.

Seq 4

MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVN

KDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

a)

b)

c)

d)