Bioinformatics Answers

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)

1. For each seq:

a) Identify the protein and species

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

of the protein?

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.

Seq1

MQVNTFSNIASMARTQVSNKKADDAKENTKDKNVQSANSSKDVDKNTLEKLNALG

GKGITQIYLVQFQQQTMNAVIGSSNAQTGLDSLLNGANLDTAKSILTNIDFASLGYSS

KNPLDMNTDELQQLVSEDGFFGVENTANRIADFVIKGGGDDVEKLKKGLEGMKKG

FEQAEKMWGGELPQISQNTIDAALKKVSDRIDELGGKTLDLQA

Seq2

MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTR

REAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

Seq3

MRLVILTLLIVGVFASNDDLWHQWKRIYNKEYKGADDDHRRNIWEQNVKHIQEHNL

RHDLGLVTYKLGLNQFTDMTFEEFKAKYLTEMPRASELLSHGIPYKANKRAVPDRID

WRESGYVTEVKDQGGCGSCWAFSTTGAMEGQYMKNEKTSISFSEQQLVDCSGP

FGNYGCNGGLMENAYEYLKRFGLETESSYPYRAVEGQCRYNEQLGVAKVTGYYT

VHSGDEVELQNLVGCRRPAAVALDVESDFMMYRSGIYQSQTCSPDRLNHGVLAV

GYGIQDGTDYWIVKNSWGTWWGEDGYIRMVRKRGNMCGIASLASVPMVAQFP

Name two traits in human two discrete variation and discontinuous variation.

Suppose you have an n×n additive matrix M with n ≥ 4, and you erase the entries

corresponding to two symmetric entries Mij and Mji in the matrix. Give an algorithm

to infer those two missing values (Mij and Mji) from the remaining data, and prove it

correct.

1.     Look at the table (right) showing survival of a group of 20 pancreatic cancer patients treated with a new drug X, compared to a control group of 20 pancreatic cancer patients who received the standard treatment and a placebo. The trial lasted for five years, which started on day 0; “lost” means that the person was lost to follow-up and did not return to the study. After 5 years everyone who was not lost to follow-up or died was known to be still alive. (20)

The RefSeq entry NM_000133.4 contains the sequence of the human mRNA coding for coagulation factor F9. The gene contains 8 coding exons and gives rise to a transcript of 2800 bp 

Next, we want to design primers to measure the expression of the F9 gene.

Go to refseq record to study its features.

Write the strategy and design the primers using primer blast .

Paste the screenshots as evidence