BIF501 Final Term Solved Questions Past Papers

BIF501-Bioinformatics-II

Solved Questions FINAL TERM (PAST PAPERS)

Q1. What is the run time of brute force algorithm?

Answer: Brute force algorithm to solve the Motif Finding problem running time of O(l · nt) . Cannot runs it on

biological samples. It is a Faster greedy techniquenot correct but have good performance. It is an

Approximation algorithm , Running time of this algorithm is O(ln2 +lnt), which is vastly better than the O(lnt)

of IMPLEMOTIFSEARCH or even the O(4lnt) of BRUTEFORCEMEDIANSTRING

Q2. What is the difference between protein sequence and DNA sequence?

DNA

Protein

A DNA sequence has a chain of nucleotides A protein sequence has chain of amino acids

The nucleotides are A, C, G and T for the DNA and A, C, G and U for RNA. There are around 20 amino acids for protein

Nucleotides are joined together through phosphodiester linkage Amino acids are join together by peptide bonds

3. What are substitution matrices? Also mention its types.

Answer: Scoring or Substitution Matrices:

It is use for scoring amino acid substitutions in pairwise alignments. They reflect substitution rates that are

originated by evolutionary events. For this we align the sequence and count the mutation at each position.

Types:

Some of the substitution matrices to compute sequence alignments are:

PAM: Point Accepted mutations BLOSUM: BLOCK

Substitution Matrix

Q4. Define suffix trees?

Answer: Suffix Trees:

It is a compressed tree containing all the suffixes and allows many problems on strings to be solved quickly.

5. What is the difference between smith water man algorithm and needle man wunshman algorithm in

term of matrix filling?

Answer: There ar two main differences between them,

Needleman-Wunsch Algorithm

1. It performs global alignment on two sequences.
2. The final step in the algorithm is the trace back for the best alignment

Start at the bottom-right corner. Follow where maximum value comes from

Smith-Waterman Algorithm

1. It is use to finds the best local alignment between two subsequences.
2. Traceback starts with maximum value in the matrix and then go backwards,

Q6. What is MATE and MATE strategy?

Answer: During fragment assembly, the reads of Sequences whose suffix and prefix are overlapping and they are

likely to be consecutives are called as mate fragments or simply mates.

Mates strategy:

Overlap: Finding potentially overlapping reads

Layout: Finding the order of reads along DNA

Consensus: Deriving the DNA sequence from layout Best match between the suffix of one read and the prefix

of another. By using this strategy we can sequence the whole fragment into single genome. Large number of

reads to ensure that experimental errors are reduced to minor noise.

Q7. Which algorithm avoid the back tracking?

Answer: Ans: KMP Algorithm:

A linear time algorithm for string matching which does not involve backtracking of strings Is called KMP

algorithm.

Q8. What would be the lexicographic order of, (TAT,ATG,TGG,GGT,GTG,TGC) ?

Answer: Lexicographic order of that spectrum is , ATG,GGT,GTG, TAT, TGC, TGG

Q9. l=3, TATGGTGC find the spectrum?

Answer: If l = 3 and s = TATGGTGC, then its spectrum will be as follow,

Spectrum(s, l) = {TAT, ATG, TGG, GGT, GTG, TGC}

and its Lexicographic order will be,

Lexicographic order, like ATG,GGT,GTG, TAT, TGC, TGG

Q10. What is denovo protein sequencing?

Answer: It is used for the protein that are not present in any data base, So its sequence is not known.

Or if it is known then it may be modified by some mutation or by some chemical modification.

Q11. Explain Primary Tertiary and Quaternary Structure of Protein?

Primary Structure: the primary structure of a protein is the linear sequence of amino acids. Together, this linear sequence is referred to as a polypeptide chain. The amino acids in the primary structure are held together by covalent bonds, which are made during the process of protein synthesis (translation).

Tertiary Structure: the tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure.

Quaternary Structure: Protein quaternary structure is the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organisations from simple dimers to large homo oligomers and complexes with defined or variable numbers of subunits.

12. Discus RNA (10) RNA Structure and types and SecondaryStructure and Process? (10)

RNA, abbreviation of ribonucleic acid, complex compound of high molecular weight that functions in cellular protein synthesis and replaces DNA (deoxyribonucleic acid) as a carrier of genetic codes in some viruses. RNA consists of ribose nucleotides (nitrogenous bases appended to a ribose sugar) attached by phosphodiester bonds, forming strands of varying lengths. The nitrogenous bases in RNA are adenine, guanine, cytosine, and uracil, which replaces thymine in DNA. RNA Structure: RNA is typically single stranded and is made of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and a phosphate group.

Q13. Supervised and Unsupervised Machine Learning?

Supervised: Supervised Learning Prediction of future cases Knowledge extraction Compression Outlier detection. Un Supervised: Learning “what normally happens” No output. Clustering: Grouping similar instances. Applications Customer segmentation in CRM Image compression Bioinformatics.

Q14. Swiss Port?

Swissport International Ltd. is the world's largest ground handling company, Swissport's activities encompass everything an airline needs on the ground to move passengers and cargo efficiently and safely. The company also performs such services as line maintenance, aircraft cleaning, and fueling.

Q15. Secondary Structure prediction process?

Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the local secondary structures of proteins based only on knowledge of their amino acid sequence.

Q16. Mate Pair Sequencing Strategy Sequencing?

Mate-pair sequencing can also provide a powerful alternative for whole genome sequencing as the longer DNA fragments can be used to bridge together DNA fragments even in the presence of highly repetitive DNA sequences which are rife in human and many other complex genomes.

Q17. Homology, Paralogy and Orthalogy? Homology Modeling?

Homology modeling, also known as comparative modeling of protein, refers to constructing an atomicresolution

orthology and paralogy relationships between two sequences are derived from such trees based on which evolutionary event (speciation or duplication, respectively) is assigned for their last common ancestor.

Q18. What method used for sequence?

DNA sequencing methodsFred Sanger and Walter Gilbert Cells make copies of DNA DNA fragments of different lengthsif one base is missing.

Q19. Limitation of AB intio?

Computationally expensive • Suitable for proteins with less than 100 residues. Conclusion • Ab initio methods rely on computing the energies of folded proteins • The protein structures with the lowest energy are deemed as plausible predictions.

Q20. Challenge of AB intio?

Very hard to accurately describe energy functions that can reliably discriminate native and non-native structures. Enormous amount of computations.

Q21. Two target discovery approaches?

Target discovery to clinical application saga • Physiology-based approach • Target-based approach.

Physiology-based approach Is a disease-centric approach in which target is not identified, multiple targets are involved. In vivo screening is done by using drugs, siRNAor antisense oligonucleotides.

Target-centric approach Target based discovery starts with the identification of genes and their protein products. Aim to develop drugs affecting one gene or a molecular mechanism.