bioinformatics platings Flashcards
If you want to examine the threedimensional structure of a protein, you will
look into which database?
PDBe
This is the process of identifying locations of genes, all the protein coding regions, and the regulatory sequences in a genome
Genome annotation
In a sequence alignment, a dot between
matched bases indicates
non-identical bases
In pairwise sequence alignments, gaps are more often seen in Local alignments than in global alignments.
False
When you get a BLAST result for a DNA
sequence, the Graphic Summary refers to
red bars specifying sequences found in the database that aligns to your sequence
You have sequenced five PCR products of DNA samples of Escherichia coli you have isolated from clinical specimens. You want to determine in which nucleotide bases the five DNA sequences vary, which tool will
be most helpful to you?
MUSCLE
If you want to compare the amino acid
sequence of your protein with those that are stored in the databases, which tool will you use?
BLASTp
When you search GenBank for the DNA
sequence of gene X, you will find a link
called FASTA. This refers to
a nucleic acid or protein sequence
represented by single-letter codes
Sequence alignment helps scientists to
- trace out evolutionary relationships
- infer the functions of newly
synthesized genes - predict new members of gene
families
Which of the following is a nucleotide
sequence database?
EMBL
It is a diagram representing evolutionary relationships among organisms
Phylogenetic tree
This is a unique identifier given to a DNA or protein sequence record to allow tracking of different versions of that sequence and the associated sequence overtime in a single
data repository
Accession number
If you are studying a set of all RNA
molecules in a mouse, you are dealing with
Transcriptomics
The alignment procedure that tries to align regions with high level of matches without considering the alignment of the rest of the sequences.
Local alignment
An example of global sequence alignment
ADLGAVFALCDRYFQ
I I I I I I I I I I I
ADLGRTQN-CDRYYQ
How many primers are needed for a successful PCR of a gene that is common among different species?
Two
Which of the following may result in no band or faint band in agarose gel electrophoresis?
-The annealing temperature is too high
(Low Ta causes non-specific binding of
primers to target, forming non-specific
bands)
Which is true about the reverse primer?
-It is the complement of the 3-prime end of the sense DNA template
What is the effect of homology between the three-prime ends of the forward and reverse
primer?
Formation of primer dimer
The primers used in polymerase chain
reaction are
Single-stranded DNA oligonucleotide
If the primer sequence is TCG, which
section of the DNA will it anneal to?
AGC
How many primers are needed for a
successful PCR of a gene when the only
information available is the protein amino amino sequence?
more than four
How many primers are needed for a
successful PCR of a known sequence of a gene?
two
(You only need one forward and one reverse
primer.)
What would be the expected effect on a PCR reaction if the primers used were slightly shorter and more variable than the intended oligonucleotide sequences?
The reaction would yield a mixture of nonspecific products.
