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101.	Which of the following is not an advantage of Statistical models’ methods in analyzing protein motifs?(a) Sequence information is preserved from a multiple sequence alignment and expresses it with probabilistic models(b) Statistical models allow partial matches and compensate for unobserved sequence patterns using pseudo-counts(c) Statistical models have stronger predictive power than the regular expression based approach, even when they are derived from a limited set of sequences(d) The comparative flexibility is less in case of these methods when compared to regular expressions methodsI had been asked this question in an online interview.Origin of the question is Motif and Domain Databases Using Statistical Models in portion Sequence Alignment of Bioinformatics
Answer» Right choice is (d) The comparative flexibility is less in case of these methods when compared to regular expressions methods The best explanation: The major limitation of regular expressions is that this method does not take into account sequence probability information about the multiple alignment from which it is modeled making them less flexible. If a regular expression is derived from an INCOMPLETE sequence set, it has less predictive power because many more SEQUENCES with the same type of motifs are not represented. UNLIKE regular expressions, position-specific SCORING matrices (PSSMs), profiles, and HMMs preserve the sequence information from a multiple sequence alignment and express it with probabilistic MODELS.

102.	Emotif uses which databases for alignment of sequences?(a) BLOCKS and PRINTS databases(b) PROSITE(c) BLOCKS(d) PRINTSI have been asked this question by my college director while I was bunking the class.I want to ask this question from Motif and Domain Databases Using Regular Expressions in chapter Sequence Alignment of Bioinformatics
Answer» Correct choice is (a) BLOCKS and PRINTS DATABASES The explanation is: Emotif is a motif database that uses multiple sequence alignments from both the BLOCKS and PRINTS databases with an ALIGNMENT collection much LARGER than PROSITE. It IDENTIFIES patterns by allowing fuzzy matching of regular expressions. Therefore, it produces fewer false negatives than PROSITE.

103.	Which of the following is not a characteristic of Fuzzy or approximate matches in regular expression?(a) This method is able to include more variant forms of a motif with a conserved function(b) the rule of matching is based on observations, not actual assumptions(c) with the more relaxed matching, there is increase of the noise level and false positives(d) the rule of matching is based on assumptions not actual observationsI have been asked this question in an interview for job.My doubt stems from Motif and Domain Databases Using Regular Expressions topic in portion Sequence Alignment of Bioinformatics
Answer» The correct option is (b) the rule of matching is based on observations, not actual assumptions Easy explanation: The rule of matching is based on assumptions not actual observations in Fuzzy or approximate matches in regular expression. This PROVIDES more PERMISSIVE matching by allowing more flexible matching of RESIDUES of similar biochemical properties. For example, if an ORIGINAL alignment only contains phenylalanine at a particular position, fuzzy matching allows other aromatic residues (including unobserved TYROSINE and tryptophan) in a sequence to match with the expression.

104.	What does this representation mean- R.L.[EQD]?(a) An arginine- Amino acid- Leucine- Amino acid- Either Apartic acid, glutamic acid or glutamine(b) An arginine- Leucine- Either Apartic acid, glutamic acid or glutamine(c) An arginine- Leucine- Amino acid- Either Apartic acid, glutamic acid or glutamine(d) An arginine- Leucine- Apartic acid and glutamic acid and glutamineI have been asked this question during an online exam.Enquiry is from Motif and Domain Databases Using Regular Expressions in chapter Sequence Alignment of Bioinformatics
Answer» Correct option is (a) An arginine- Amino acid- Leucine- Amino acid- EITHER Apartic acid, GLUTAMIC acid or glutamine For EXPLANATION I would say: This is an EXAMPLE of pexel motif. Here, the ‘.’ represents the ‘end’ i.e. the amino acid as mentioned in the ANSWER and the [ ] means ‘or’ i.e. either of the mentioned residue is present in the given position.

105.	Which of the following best defines regular expressions?(a) They are made up of terms, operators and modifiers(b) They describe string or set of strings to find matching patterns(c) They are strictly restricted to alignment and corresponding score(d) They consist of set of rules for the connotations of various amino acid residuesI had been asked this question during a job interview.This interesting question is from Motif and Domain Databases Using Regular Expressions topic in chapter Sequence Alignment of Bioinformatics
Answer» The correct option is (b) They DESCRIBE string or set of strings to find matching patterns For EXPLANATION: REGULAR expressions are powerful notable algebra that describe string or set of strings to find matching patterns. Pattern matching is defined as true or false in answer or outcome. And it is true that they are made up of terms, operators and modifiers but they are TERMINOLOGIES further used in matching PROCESS.

106.	In terminologies related to regular expressions which of the following is false about terms and operators?(a) Terms are strings or substrings(b) Operators combine terms and expressions(c) Operators do not have precedence(d) Operators have precedence like arithmetic operatorsThe question was asked during a job interview.This key question is from Motif and Domain Databases Using Regular Expressions in chapter Sequence Alignment of Bioinformatics
Answer» Correct CHOICE is (c) Operators do not have PRECEDENCE Easy EXPLANATION: For harmonious, efficient and error-free functioning of the MATCHING preocess, operators have precedence in order to SET the priority of the operations to be carried out during the alignment.

107.	While analysing motif sequences, what is the major disadvantageous feature of PROSITE?(a) The database constructs profiles to complement some of the sequence patterns(b) The functional information of these patterns is primarily based on published literature(c) Some of the sequence patterns are too short to be specific(d) Lack of specificity about probability and variation and relation between themI had been asked this question in quiz.The origin of the question is Motif and Domain Databases Using Regular Expressions topic in section Sequence Alignment of Bioinformatics
Answer» The correct answer is (C) Some of the sequence patterns are too short to be SPECIFIC The best EXPLANATION: The major pitfall with the PROSITE patterns is that some of the sequence patterns are too short to be specific. Rest of the options are advantages. The PROBLEM with these short sequence patterns is that the resulting match is very likely to be a result of random events. Overall, PROSITE has a greater than 20% error rate. Thus, either a match or non-match in PROSITE should be treated with caution.

108.	On average, what is the length of a typical domain?(a) About 100 residues(b) About 300 residues(c) About 500 residues(d) About 900 residuesThe question was asked in homework.Origin of the question is Protein Motifs and Domain Prediction in chapter Sequence Alignment of Bioinformatics
Answer» Correct option is (a) About 100 residues Best explanation: The predicted optimal NUMBER of residues, which corresponds to the maximum free energy of UNFOLDING, is 100. This is in agreement with a STATISTICAL analysis derived from their experimental structures of motifs. For too short chain, change in enthalpy of internal interactions is not favorable enough for folding because of the limited number of inter-residue contacts. And a long chain is also unfavorable for a single DOMAIN.

109.	Which of the following is false about the ‘loop’ structure in proteins?(a) They connect helices and sheets(b) They are more tolerant of mutations(c) They are more flexible and can adopt multiple conformations(d) They are never the components of active sitesI got this question in a job interview.I want to ask this question from Protein Motifs and Domain Prediction in chapter Sequence Alignment of Bioinformatics
Answer» Correct choice is (d) They are NEVER the components of active sites Easiest EXPLANATION: Loops are frequently components of active sites as they are flexible in nature and as they are situated on the SURFACE of the structure. Besides, they vary in length and 3-D CONFIGURATIONS which GIVE even more chances to be component of active sites.

110.	In the zinc finger, which residues in this sequence motif form ligands to a zinc ion?(a) Cysteine and histidine(b) Cysteine and arginine(c) Histidine and proline(d) Histidine and arginineThe question was asked during an internship interview.This is a very interesting question from Protein Motifs and Domain Prediction in chapter Sequence Alignment of Bioinformatics
Answer» Right option is (a) Cysteine and histidine To explain: In the zinc FINGER, which is found in a widely VARYING FAMILY of DNA-binding proteins, cysteine and histidine residues in this SEQUENCE motif form ligands to a zinc ion whose coordination is essential to stabilize the TERTIARY structure.

111.	Which of the following is not an advantageous feature or algorithm of the database PRINTS?(a) This program breaks down a motif into even smaller non-overlapping units called ‘fingerprints’, which are represented by unweighted PSSMs(b) To define a motif, at least a majority of fingerprints are required to match with a query sequence(c) A query that has simultaneous high-scoring matches to a majority of fingerprints belonging to a motif is a good indication of containing the functional motif(d) The difficulty to recognize short motifs when they reach the size of single fingerprintsThis question was addressed to me during a job interview.Asked question is from Motif and Domain Databases Using Statistical Models in portion Sequence Alignment of Bioinformatics
Answer» The correct choice is (d) The difficulty to recognize SHORT motifs when they reach the size of single fingerprints To explain I WOULD say: PRINTS is a protein fingerprint database CONTAINING ungapped, MANUALLY curated ALIGNMENTS corresponding to the most conserved regions among related sequences. The drawbacks of PRINTS are–the difficulty to recognize short motifs when they reach the size of single fingerprints and a relatively small database, which restricts detection of many motifs.

112.	For motif scanning which of the following programs or databases is for regulated sites curated from scientific literature?(a) ENSEMBL(b) ORegAnno(c) MAST(d) CloverThe question was asked in a job interview.The above asked question is from Motif and Domain Databases Using Statistical Models in portion Sequence Alignment of Bioinformatics
Answer» RIGHT choice is (b) ORegAnno Best explanation: Clover identifies overrepresented motifs in protein sequences whereas; MAST allows users to scan DIFFERENT databases for matches to motifs. ENSEMBL is another online GENOMIC sequence repository which also includes online TOOLS for data mining as well as BLAST searches.

113.	In regular expressions, which of the following pair of pattern is wrongly matched with its significance?(a) [ ] – Or(b) { } – Not(c) ( ) – Repeats(d) Z – AnyThe question was asked by my school teacher while I was bunking the class.My question is based upon Motif and Domain Databases Using Regular Expressions topic in chapter Sequence Alignment of Bioinformatics
Answer» The correct answer is (d) Z – Any The explanation: Regular EXPRESSION SYMBOLS have their own significances in regular expressions systemmeans [GA] .g.e rFo ‘G or A’, {V,P} MEANS not P or V, x(4) means (xxxx). LIKEWISE, X denotes any character.

114.	Motifs that can form α/β horseshoes conformation are rich with which protein residue?(a) Proline(b) Arginine(c) Valine(d) LeucineThe question was posed to me in quiz.I need to ask this question from Protein Motifs and Domain Prediction topic in portion Sequence Alignment of Bioinformatics
Answer» RIGHT answer is (d) Leucine To elaborate: Specific pattern of Leucine residues, strands form a curved sheet with helices on the outside. Leucine-rich repeats (LRRs) are 20-29-residue SEQUENCE motifs present in a number of proteins with diverse functions. The PRIMARY function of these motifs APPEARS to be to provide a versatile STRUCTURAL framework for the formation of protein-protein interactions.

115.	Which of the following is not a characteristic of exact matches in regular expression?(a) There must be a strict match of sequence patterns(b) Any variations in the query sequence from the predefined patterns are not allowed(c) Provide more permissive matching by allowing more flexible matching of residues of similar biochemical properties(d) Searching a motif database using this approach results in either a match or non-matchThis question was posed to me in final exam.My question is from Motif and Domain Databases Using Regular Expressions in portion Sequence Alignment of Bioinformatics
Answer» Correct answer is (c) Provide more permissive matching by allowing more flexible matching of residues of similar biochemical properties To explain I WOULD say: In this type of matching, there has to be a STRICT match of SEQUENCE patterns. This way of searching has a good chance of missing truly relevant motifs that have slight variations, thus generating false-negative results. As NEW sequences of motif are being accumulated, the rigid regular expression tends to become obsolete if not updated regularly to reflect the changes.

116.	Which of the following least describes Long Loop β-hairpins?(a) They are Often referred to as a ‘random coil’ conformation(b) Generally they are referred to as the β-meander supersecondary structure(c) Loop looks similar to the Greek Letter Ω(d) Wide-range of conformations with very specific sequence preferencesThe question was posed to me in a job interview.I need to ask this question from Protein Motifs and Domain Prediction in section Sequence Alignment of Bioinformatics
Answer» The correct option is (d) Wide-range of conformations with very specific sequence PREFERENCES The explanation: They are wide-range of conformations with no particular sequence preferences. As the NAME SUGGESTS ‘meander’ the conformation they possess is also QUITE unspecified. Addition to that Long loop β-hairpins are special case of Ω loops, that explains a LOT about their structural preferences.

117.	Which of the common structural motifs are described wrongly?(a) β-hairpin – adjacent antiparallel strands(b) Greek key – 4 adjacent antiparallel strand(c) β-α-β – 2 parallel strands connected by helix(d) β-α-β – 2 antiparallel strands connected by helixI got this question in final exam.I want to ask this question from Protein Motifs and Domain Prediction topic in portion Sequence Alignment of Bioinformatics
Answer» Right choice is (d) β-α-β – 2 ANTIPARALLEL strands connected by HELIX To elaborate: In motif, two adjacent βparallel strands are connected by an α helix from the C-terminus of strand 1 to the N-terminus of strand. Most protein structures that CONTAIN parallel beta-sheets are built up from COMBINATIONS of such β-α-βmotifs.

118.	While scanning for similarities in motifs, how regular expressions’ techniques work?(a) It represents a sequence family by a string of characters and further compares them(b) An algorithm similar to dynamic programming is used(c) Dot matrix analysis is used in this type of sequence analysis(d) Matrix analysis methods are used in this typeThis question was addressed to me in semester exam.Origin of the question is Motif and Domain Databases Using Regular Expressions topic in division Sequence Alignment of Bioinformatics
Answer» Correct answer is (a) It REPRESENTS a SEQUENCE family by a string of characters and further compares them To ELABORATE: In regular expressions’ techniques Pattern matching is defined as true or false in answer or outcome. In other words, if the pattern described in regex is found in a string of LETTERS, the answer is true.

119.	Which of the following is not the function of Short Linear Motifs?(a) Irreversible cleavage of the peptide at the SLiM(b) Reversible cleavage of the peptide at the SLiM(c) Moiety addition at targeted sites on SLiM(d) Structural modifications of the peptide backboneThis question was posed to me in examination.Question is from Protein Motifs and Domain Prediction topic in portion Sequence Alignment of Bioinformatics
Answer» The correct answer is (a) Irreversible cleavage of the peptide at the SLiM For explanation: Short LINEAR MOTIFS are short stretches of protein sequence that MEDIATE protein-protein interaction. SLiMs can act as recognition sites of endo-peptidases RESULTING in the irreversible cleavage of the peptide at the SLiM.

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