ICAR-IASRI MSc and PhD (Agricultural Statistics, Computer Application, Bioinformatics) · India · ICAR-Indian Agricultural Statistics Research Institute with the IARI Graduate School
Original practice questions written to the published syllabus · not past papersThe third sub-subject of the ICAR Statistical Sciences group: molecular-biology basics, sequence databases, pairwise and multiple alignment, genome assembly, phylogenetics, and the statistics behind scoring and tree reliability. Taught from the statistician's side of the bench.
In the exams: AICE-JRF subject 69 Bioinformatics Units 1-5 (heavy: the whole paper); AIEEA-PG Group 07 sub-subject 7.3 (heavy); AIEEA-PG Group 07 bioinformatics databases (present)
How our questions for ICAR-IASRI MSc and PhD spread across the units of Bioinformatics & Computational Biology. Difficulty: 11 easy, 7 medium, 1 hard.
| Molecular biology basics: DNA, RNA, gene expression and recombinant DNA | 8 | |
| Genomic resources and databases: NCBI, EBI, ExPASy, GenBank, EMBL, DDBJ | 6 | |
| Protein structure and functional annotation (introduction) | 2 | |
| Pairwise alignment: Needleman-Wunsch and Smith-Waterman | 1 | |
| BLAST and FASTA; scoring matrices PAM and BLOSUM | 1 | |
| Sequencing technologies and genome assembly: de novo and comparative | 1 |
Choose an answer, then open the working. Each explanation says why the right answer is right and why the others are not.
A double-stranded DNA sample has 30% adenine. What percentage is guanine?
D. 20%
By Chargaff's rules A = T = 30%, so G + C = 40% and G = C = 20%.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
How many reading frames must be examined to search a double-stranded DNA sequence for open reading frames?
C. Six
Three frames on each strand, so six in total; searching only the given strand misses genes on the complementary strand.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
Using the Wallace rule, what is the approximate melting temperature of a 20-base primer with 10 G or C and 10 A or T bases?
C. 60 °C
Tm ≈ 2(A + T) + 4(G + C) = 2 × 10 + 4 × 10 = 60 °C. The rule is only a rough guide for short oligonucleotides.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
Which three databases form the International Nucleotide Sequence Database Collaboration?
C. GenBank, ENA and DDBJ
GenBank (NCBI, USA), the European Nucleotide Archive (EMBL-EBI) and the DNA Data Bank of Japan exchange data daily. UniProt and PDB hold proteins and structures.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
Which organisation maintains GenBank?
D. NCBI
GenBank is maintained by the National Center for Biotechnology Information. ENA is at EMBL-EBI; ExPASy belongs to the SIB.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
How does the header line of a FASTA file begin?
C. With the character '>'
FASTA headers start with '>'; FASTQ records start with '@'; GenBank flat files begin with LOCUS.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
How many lines make up one read record in a FASTQ file?
B. Four
Identifier line (@), sequence, '+' line, and quality string of the same length as the sequence.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
In IUPAC nucleotide codes, what does the letter R represent?
C. A or G (a purine)
R = purine (A/G), Y = pyrimidine (C/T), N = any base.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
In a dot plot of a sequence against itself, what do short diagonals parallel to the main diagonal indicate?
B. Repeated segments within the sequence
Off-diagonal lines show where one part of the sequence matches another: internal repeats.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
Which level of protein structure is the arrangement of several polypeptide chains in a complex?
D. Quaternary
Primary is the sequence, secondary the local helices and sheets, tertiary the fold of one chain, quaternary the assembly of subunits.
Further reading: Durbin et al., Biological Sequence Analysis; Mount, Bioinformatics; Pevsner, Bioinformatics and Functional Genomics; Felsenstein, Inferring Phylogenies
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