Bioinformatics Answers

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

Access any flatfile from NCBI (The NCBI home page is http://www.ncbi.nlm.nih.gov ). Decode every information given in the accessed file

•       What is the first line indicating

•       What is the nature of the sequence

•       Identify the version

•       Is the data you have accessed is coding sequences or open reading frame? Which is the start and stop codon?

•       Has it got untranslated regions?

•       Has it been linked to the protein database? If connected, how many amino acids? What is the accession number?

•       Is the information published?

Calculate 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 W(L) = -2L

 Tiny openings or pores in plant tissue that allow for gas exchange

The PAM matrices are considered nonreciprocal, meaning that the probability of changing an amino acid such as alanine to arginine is not equal to the probability of changing an arginine to an alanine. Why?

Retrieve the following information of the given mouse genes : PGK1 , GAPDH , Alpha - globin , Insulin ; Gene ID , No. of Exons and Introns , CDS length & Introns length , Protein ID , Amino Acids sequence length . Present all the information in a tabular format. Sequences should be retrieved in both GenBank and Fasta Format.