Genomic Databases and Tools

Question 1

Which of the following software programmes allows you to input a DNA sequence and search for match from the protein database?

Answer 1

a) Blastn
b) Blastp
c) Blastx
d) Tblastn
e) Tblastx

Question 2

A protein reference sequence in the NCBI Protein Database will have an accession number that starts with which of the following?

Answer 2

a) NM_
b) NP_
c) NR_
d) PN_
e) PR_

Question 3

Which of the answers below describes the following sequence?
>NP_057457.1 WW domain-containing oxidoreductase isoform 1 [Homo sapiens]
MAALRYAGLDDTDSEDELPPGWEERTTKDGWVYYANHTEEKTQWEHPKTGKRKRVAGDLPYGWEQETDEN
GQVFFVDHINKRTTYLDPRLAFTVDDNPTKPTTRQRYDGSTTAMEILQGRDFTGKVVVVTGANSGIGFET
AKSFALHGAHVILACRNMARASEAVSRILEEWHKAKVEAMTLDLALLRSVQHFAEAFKAKNVPLHVLVCN
AATFALPWSLTKDGLETTFQVNHLGHFYLVQLLQDVLCRSAPARVIVVSSESHRFTDINDSLGKLDFSRL
SPTKNDYWAMLAYNRSKLCNILFSNELHRRLSPRGVTSNAVHPGNMMYSNIHRSWWVYTLLFTLARPFTK
SMQQGAATTVYCAAVPELEGLGGMYFNNCCRCMPSPEAQSEETARTLWALSERLIQERLGSQSG

Answer 3

a) Nucleotide sequence in FASTA format.
b) Protein sequence in FASTA format.
c) Nucleotide sequence in GenBank format.
d) Protein sequence in GenBank format.
e) None of the above.

Question 4

In PCR primer design, which of the following primer features is most likely to result in the formation of secondary structures in the primer, or binding of primers together, and thus inhibit the amplification of the target gene?

Answer 4

a) A high 3’-complementarity score.
b) A low 3’-complementarity score.
c) A high GC content.
d) A low GC content.
e) A high melting (annealing) temperature.