BIF401 Midterm Solved Past Paper

MUHAMMAD IMRAN · BIF401-Bioinformatics-I · PAST PAPER SOLVED · MID TERM

Rooted and Un-rooted phylogentic tree?

Rooted and Unrooted trees can be used to show phylogenetic relationships between sequences • Several types of algorithms exist which are divided into two classes.

Purpose of bowie algorithm?

Fold Recognition/Threading Online Tools for Fold Recognition GOR Algorithm Homology Modelling 3D-1D Bowie Algorithm Machine Learning Approaches to Structure Prediction Neural Networks for Structure Prediction PSIPRED Introduction to Hidden Markov Models Ab initio modeling. (PPT)

Complete protein sequence? F-x(3)-X-R-F-K-X (4-5) –D-E-R

FXXXXRFKXXXXXDER (not sure)

Enlist salient Feature of block diagram of mass spectrum?

A mass spectrum is a plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical structures of molecules and other chemical compounds.

What does uni port sequence give information about protein query?

Types and Function of RNA?

Three major types of RNA are mRNA, or messenger RNA, that serve as temporary copies of the information found in DNA; rRNA, or ribosomal RNA, that serve as structural components of proteinmaking structures known as ribosomes; and finally,tRNA, or transfer RNA, that ferry amino acids to the ribosome to be assembled.

Protein folding?

Protein folding is the physical process by which a protein chain acquires its native 3-dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner.

Chou Fasman Algorithm?

The Chou–Fasman method is an empirical technique for the prediction of secondary structures in proteins, originally developed in the 1970s by Peter Y. Chou and Gerald D. Fasman.

Protein sequence and database name?

protein or peptide. The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. ... The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

pH less than pK?

If the pH is less than the pKa, then the acid form of the compound predominates. If the pH is greater than the pKa, then the conjugate base predominates. This is shown graphically here: Most ionizable groups fallinto two patterns depending on the charge found on the acidic form.

Difference between RNA and DNA with ref. to nucleotide?

Nucleotide[edit] A nucleotide is composed of a nucleobase (nitrogenous base), a five-carbon sugar (either ribose or 2'-deoxyribose), and one to three phosphate groups. ... In DNA, the purine bases are adenine and guanine, while the pyrimidines are thymine and cytosine. RNA uses uracil in place of thymine.

Redundancy codon, name an amino acids which coded for three different codon?

Phylogenetic tree types?

Scaled Trees: Branch lengths are equal to the magnitude of change in the nodes. Unscaled Trees: Only representing the relationship between sequences.

Purpose of uni port and their feature?

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.

What do you know about rammananchandrah plot?

Ramachandran Plot is a way to visualize dihedral angles ψ against φ of amino acid residues in protein structure. Ramachandran recognized that many combinations of angles in a polypeptide chain are forbidden because of steric collisions between atoms.

Blastx and tblastx work?

Blastx: Search protein database using translated nucleotide query. Tblastx: Search translated nucleotide database using translated nucleotide query.

How we can modify dot plot to consider and mis match in alignment?

In the Alignment View locate the first region of mismatch in your alignment. Turn on the ... Youshould realign these sequences with modified settings. Rather than ... In the Dotplot there is also an inverted region (you will need to activate the. Reverse ... sequences and do you think it is a fair representation of their sequence.

Why do we need to use dynamic programming in predicting RNA structure?

RNA sequences comprises of 4 types of nucleotides • G/C, G/U & A/U are complementary & can form H-bonds

• RNA sequences may contain hundreds of nucleotides, hence many combinations are possible. • So, given an RNA sequence, there is a large number of possible 2’ structures • This presents us with an extremely complex and large problem

Few challenges in field of biotechnology?

Bioinformatics is full of challenges and opportunities. • Amongst other frontiers in bioinformatics, there are protein structures, systems biology and personalized medicine!

Step to use FASTA?

Step 1: Specify the tool input (sequence and database). Step 2: Entering of input sequence. Step 3: Set up the parameters. Step 4: Submit the query for processing.

Difference between local and global alignment?

Global alignment - maximizes the number of matches between the query and source sequences along the entire length of both the sequences. Local alignment - gives the highest scoring local match between both query and sequences

Domain of protein?

Domains are semi-independent functional structures in a protein • Protein may contain multiple domains • Hence, we can try to classify proteins by their domains. Examples of Protein Domains 1. Alpha Domains 2. Beta Domains 3. Alpha/Beta Domains 4. Alpha + Beta Domains 5. Alpha & Beta Multi-Domains 6. Membrane & cell-surface proteins

Uni port three main functions?

Scoring matrix in detail?

Scoring Matrix. Scoring matrices are used to determine the relative score made by matching two characters in a sequence alignment. ... There are many flavors of scoring matrices for amino acid sequences, nucleotide sequences, and codon sequences, and each is derived from the alignment of "known" homologous sequences.

PAM matrix in detail?

Alignment scoring matrices are very useful in giving suitable scores to matches and mismatches • There are 2 types of scoring matrices i.e. PAM and BLOSUM • PAM means “Point Accepted Mutations” • Point accepted mutation is a substitution of one amino acid by another such that the protein functions stays conserved. PAM unit is a time in which about 1% of amino acids in a sequence undergo accepted mutations.

Bioinformatics Promise?

Draw the structure of RNA and DNA?

Newick notation example?

Complete protein sequence formula 3 role of 5’cap and 3’cap?

Dot plot matrix?

Dot plots employ dot matrix with two sequences plotted on top & left of the matrix • Matches are represented by dots • Dots on diagonals are connected and represent alignments.

Formula of sequence?

Write field of bioinformatics?

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinaryfield of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data.

How bulge formed?

Bulges, are formed when a double-stranded region cannot form base pairs perfectly. • Bulges can be asymmetric with varying number of base pairs on one side of the loop.

Why need dynamic programming?

Dynamic programming is both a mathematical optimization method and a computer programmingmethod. ... Likewise, in computer science, if a problem can be solved optimally by breaking it into sub-problems and then recursively finding the optimal solutions to the sub-problems, then it is said to haveoptimal substructure.

Why diagonal form energy matrix of zuker algorithm?

Find out the mis match match and gap final score?

Code of protein sequence ATCATCCATAC?

Basic principle for progressive alignment for MSA?

Progressive alignment methods are efficient enough to implement on a large scale for many (100s to 1000s) sequences. ... They recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments. They offer different MSA tools forprogressive DNA alignments.

How pseudo knot effect RNA?

The pseudoknot is a potentially important tertiary structural motif of RNA.

How many type of data base in bioinformatics and What type of information they contain?

These formats include text, sequence data, protein structure and links. Each of these can be found from certain sources, for example: Text formats are provided by PubMed and OMIM. Sequence data is