Bioinformatics Mcqs

Page No. 4

Which of the following statements about CATH-Gene3D and HAMAP databases is incorrect regarding its features?


aCATH-Gene3D describes protein families and domain architectures in complete genomes


bIn CATH-Gene3D the functional annotation is provided to proteins from single resource


cHAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded proteins families or subfamilies.


dHAMAP stands for High-quality Automated and Manual Annotation of microbial Proteomes



Which of the following statements about PRINTS and ProDom databases is incorrect regarding its features?


aPRINTS is a compendium of protein fingerprints


bUsually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space


cCurrent versions of ProDom are built using a novel procedure based on recursive BLAST searches


dProDom domain database consists of an automatic compilation of homologous domains



Which of the following statements about SUPERFAMILY database is incorrect regarding its features?


aSequences can be submitted raw or FASTA format


bSequences must be submitted in FASTA format only


cIt searches the database using a superfamily, family, or species name plus a sequence, SCOP, PDB or HMM ID’s


dIt has generated GO annotations for evolutionarily closed domains and distant domains



What is the source of protein structures in SCOP and CATH?


aUniprot


bProtein Data Bank


c Ensemble


dInterPro


View Answer InterPro

Which of the following statements about SCOP is incorrect regarding its features?


aProteins with the same shapes but having little sequence or functional similarity are placed in different super families, and are assumed to have only a very distant common ancestor


b Proteins having the same shape and some similarity of sequence and/or function are placed in ‘families’, and are assumed to have a closer common ancestor


cSCOP was created in 1994 in the Centre of Protein Engineering and the University College London


d It aims to determine the evolutionary relationship between proteins



Which of the following is not a member database of InterPro?


aSCOP


bHAMAP


cPANTHER


dPfam


View Answer SCOP

Pfam is available at four locations around the world. Which of the following is not one of them?


aUK


bSweden


cUS


dJapan


View Answer Japan

Which of the following statements about InterPro is incorrect regarding its features?


aProtein relatedness is defined by the P-values from the BLAST alignments


b The most closely related sequences are grouped into the lowest level clusters


cMore distant protein groups are merged into higher levels of clusters


d The outcome of this cluster merging is a tree-like structure of functional categories



Which of the following statements about COG is incorrect regarding its features?


aCurrently, there are 4,873 clusters in the COG databases derived from unicellular organisms


b It is constructed by comparing protein sequences encoded in forty-three completely sequenced genomes, which are mainly from prokaryotes, representing thirty major phylogenetic lineages


cThe interface for sequence searching in the COG database is the COGnitor program, which is based on gapped BLAST


dIt is a protein family database based on structural classification



Which of the following is wrong in case of substitution matrices?


aThey determine likelihood of homology between two sequences


bThey use system where substitutions that are more likely should get a higher score


c They use system where substitutions that are less likely should get a lower score


dBLOSUM-X type uses logarithmic identity to find similarity



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