Bioinformatics Mcqs

Page No. 3

Which of the following is false in case of the CDART and its algorithm?


aCDART is a domain search program that combines the results from RPS-BLAST, SMART, and Pfam

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bThe program is now an integral part of the regular BLAST search function

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cCDART is a substitute for individual database searches

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dIt stands for Conserved Domain Architecture

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View Answer CDART is a substitute for individual database searches

Which of the following is false in case of the database InterPro and its algorithm?


a InterPro is an integrated pattern database designed to unify multiple databases for protein domains and functional sites

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b\This database integrates information from PROSITE, Pfam, PRINTS, ProDom, and SMART databases

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cOnly overlapping motifs and domains in a protein sequence derived by all five databases are included

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dAll the motifs and domains in a protein sequence derived by all five databases are included

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View Answer ) This database integrates information from PROSITE, Pfam, PRINTS, ProDom, and SMART databases

Which of the following is false in case of the database SMART and its algorithm?


aContains HMM profiles constructed from manually refined protein domain alignments

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bAlignments in the database are built based on tertiary structures whenever available or based on PSI-BLAST profiles

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cAlignments are further checked but not refined by human annotators before HMM profile construction

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dSMART stands for Simple Modular Architecture Research Tool

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View Answer Alignments are further checked but not refined by human annotators before HMM profile construction

Which of the following is false in case of the database Pfam and its algorithm?


a Each motif or domain is represented by an HMM profile generated from the seed alignment of a number of conserved homologous proteins

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bSince the probability scoring mechanism is more complex in HMM than in a profile-based approach the use of HMM yields further increases in sensitivity of the database matches

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cPfam-B only contains sequence families not covered in Pfam

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dThe functional annotation of motifs in Pfam-A is often related to that in UNIPROT

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View Answer Since the probability scoring mechanism is more complex in HMM than in a profile-based approach the use of HMM yields further increases in sensitivity of the database matches

Which of the following is untrue in case of the database BLOCKS?


aThe alignments are automatically generated using the same data sets used for deriving the BLOSUM matrices

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bThe derived ungapped alignments are called ‘blocks’, which are usually longer than motifs, are subsequently converted to PSSMs

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c A weighting scheme and pseudo counts are subsequently applied to the PSSMs to account for underrepresented and unobserved residues in alignments

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dThe functional annotation of blocks is not consistent with that for the motifs

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View Answer The functional annotation of blocks is not consistent with that for the motifs

In which of the following multipurpose packages Gibbs sampling algorithm is used?


aConsensus

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bBEST

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cAlignACE

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dPhyloCon

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View Answer AlignACE

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 PSSM

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b To define a motif, at least a majority of fingerprints are required to match with a query sequence

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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

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d The difficulty to recognize short motifs when they reach the size of single fingerprints

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View Answer The difficulty to recognize short motifs when they reach the size of single fingerprints

For motif scanning which of the following programs or databases is for regulated sites curated from scientific literature?


aENSEMBL

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bORegAnno

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cMAST

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dClover

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View Answer ORegAnno

Which of the following is not an advantage of Statistical models’ methods in analyzing protein motifs?


aSequence information is preserved from a multiple sequence alignment and expresses it with probabilistic models

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bStatistical models allow partial matches and compensate for unobserved sequence patterns using pseudo-counts

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cStatistical

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d The comparative flexibility is less in case of these methods when compared to regular The comparative flexibility is less in case of these methods when compared to regular expressions methods expressions methods

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View Answer The comparative flexibility is less in case of these methods when compared to regular expressions methods

10. Which of the following statements about PANTHER and TIGRFAMs databases is incorrect regarding its features?


a TIGRFAMs provides a tool for identifying functionally related proteins based on sequence homology

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bTIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, hidden Markov models (HMMs) and annotation

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cHidden Markov models (HMMs) are not used in PANTHER d) PANTHER is a large collection of protein families that have been subdivide

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dPANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise

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View Answer Hidden Markov models (HMMs) are not used in PANTHER d) PANTHER is a large collection of protein families that have been subdivided

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