Bioinformatics
Description: Biotechnology Bioinformatics GATE Genomics and Proteomics Sequence Analysis Sequence and Structure DatabasesBioinformatics | |
Number of Questions: 25 | |
Created by: Manjit Singh | |
Tags: Biotechnology Bioinformatics GATE Genomics and Proteomics Sequence Analysis Sequence and Structure Databases |
Which of the following BLAST programs are used to study the sequence-structure-function relationship of nucleotide sequences?
- Blastp
- MEGABLAST
- Blastn
- PHI-BLAST
Which of the following statements is/are CORRECT?
- DNA microarrays are used to measure the concentration of different tRNAs in a biological sample.
- The complete set of sRNAs that are transcribed in a cell is often called its transcriptome.
- Expressed sequence tags (ESTs) are short, single-read mRNA sequences.
Which of the following statements are FALSE?
P. Paralogs are genes in different species that are diverged from a common ancestral sequence, as a result of the speciation. Q. PSI-BLAST builds profiles and performs data base searches in an iterative fashion. R. A domain may or may not include motifs within its boundaries. S. Motifs and domains are evolutionarily less conserved than other regions of a protein and tend to evolve as units.
Which of the following programs queries protein sequences to a nucleotide sequence database with the sequences translated in all six reading frames?
Which of the following programs did Pearson and Lipman searched for similarity between a protein query sequence and any group of nucleotide sequences?
P. FastA Q. TFastA R. FastX S. TFastX
Which of the following is a protein family database based on phylogenetic classification?
Which of the following are examples of progressive alignment programs?
- PRRN
- DIALIGN2
- Match-Box
- Clustal
- Poa
In which of the following cases, it is preferable to use BLASTX?
- If the input sequence is a protein-encoding DNA sequence.
- If one is looking for protein homologs encoded in newly sequenced genomes.
- If a DNA sequence is to be used as the query.
Which of the following programs is able to do both simple sequence format conversion as well as alignment format conversions?
Which of the following gene prediction programs use discriminant analysis for exon prediction?
P. FGENES Q. MZEF R. GENSCAN S. HMMgene
Which of the following statements is/are TRUE?
- Praline is more accurate than Clustal.
- Alignment at the protein level is more sensitive than at the DNA level.
- Sequence alignment at the protein level is much more informative for functional and evolutionary analysis.
Which of the following algorithms requires the user to provide a pairwise or multiple alignment as input?
- RNAalifold
- Foldalign
- Dynalign
Which of the following is a RNA database?
Which of the following are consensus-based gene prediction programs?
- GenomeScan
- EST2Genome
- SGP-1
- GeneComber
- DIGIT
Which of the following statements are FALSE regarding PSIBLAST?
- PSIBLAST uses PSSMs to score matches between query and database sequences.
- PSIBLAST is a statistically driven search method that finds regions of similarity between your query sequence and database sequences and produces ungapped alignments of those regions.
- The number of scoring matrices available for use with PSIBLAST is limited.
Which of the following scoring matrices is/are based on implicit model of evolution?
- PAM
- Gonnet
- JTT
- BLOSUM
Which of the following is a program for searching bacterial ρ-independent termination signals located at the end of operons?
Which of the following is a web-based program that uses a neural network to make promoter predictions?
Match the entries in Column - I with those in Column - II.
Group - I | |
Group - II | |
P. FGENESB | 1. A suite of gene prediction programs based on the fifth-order HMMs. |
Q. GeneMark | 2. A UNIX program from TIGR that uses the IMM algorithm to predict potential coding regions. |
R. Glimmer | 3. A web-based program specifically trained for bacterial sequences based on fifth-order HMMs for detecting coding regions |
Which of the following are phylogenetic footprinting–based methods?
P. ConSite Q. PromH(W) R. MEME S. AlignACE
Which of the following is a web-based program that uses a consensus method to identify promoter elements for human DNA?
Match the entries in Group - I with those in Group - II.
Group - I | |
Group - II | |
P. PSI-BLAST | 1. Iteratively searches one or more protein databases for sequences similar to one or more protein query sequences. |
Q. PHI-BLAST | 2. Searches for proteins that contain a pattern specified by the user AND are similar to the query sequence in the vicinity of the pattern. |
R. blastp | 3. Used for both identifying a query amino acid sequence and for finding similar sequences in protein databases. |
Match the entries in column I (Matrices) and column II (operation).
Column I | |
Column II | |
P. PAM | 1. Henikoff and Henikoff |
Q. BLOSUM | 2. Margaret Dayhoff |
R. PSSM | 3. Gary Stormo |
Which of the following is a web-based program that runs four individual motif-finding algorithms – MEME, GIBBS sampling, CONSENSUS and Coresearch, all simultaneously?
Which of the following databases integrates information from PROSITE, Pfam, PRINTS, ProDom and SMART databases?