Bioinformatics midterm
questions and answers
cDNA - answer complementary DNA; the coding
DNA sequence without introns made using RT from
mRNA
BLAT - answer (BLAST-like alignment tool) BLAT
parses an entire
genomic DNA database into words (11 k-mers),
then
searches them against a query. Thus it is a mirror
image
of the BLAST strategy. It is designed to quickly
find DNA sequences of 95% and greater similarity
of length 25 bases or more. It may miss more
divergent or shorter sequence alignments.
gene coordinate - answer chromosome start-stop
UCSC genes track - answer set of gene predictions
based on data from RefSeq, GenBank, CCDS, Rfam,
and the tRNA Genes track. It includes both protein-
coding genes and non-coding RNA genes.
systems biology - answer study of an organism,
viewed as integrated and interacting networks of
,genes, proteins and biochemical reactions which
give rise to life
genome - answer DNA sequences of all
chromosomes of an organism
bioinformatics - answer technology that uses
computers for storage, retrieval, manipulation, and
distribution of information related to biological
macromolecules (DNA, RNA, proteins, metabolites,
and lipids).
It is at the interface of biological measurement and
result
2 bioinformatics subfields - answer Development of
computational tools and databases
Application of those tools to biological problems
3 basic areas of bioinformatics research - answer
molecular sequence, structure, and function
analysis
sequence analysis - answer genome comparison,
phylogeny, gene and promoter prediction, motif
discovery, sequence database searching, sequence
alignment
, structure analysis - answer nucleic acid structure
prediction, protein structure prediction,
classification, and comparison
function analysis - answer metabolic pathway
modeling, gene expression profiling, protein
interaction prediction, protein subcellular
localization prediction
computational biology - answer Theoretical
biological model building and simulation.
database - answer digital archive used to store and
organize data (logical info organization=schema) in
such a way that information can be retrieved easily
using a variety of search criteria
biological database - answer library of life sciences
information, collected from scientific experiments,
published literature, high throughput experiment
technology, and computational analyses. They
contain information from research areas including
genomics, proteomics, metabolomics, microarray
gene expression, and phylogenetics. Information
contained in biological databases includes gene
function, structure, localization (both cellular and
chromosomal), clinical effects of mutations as well
as similarities of biological sequences and
structures.
questions and answers
cDNA - answer complementary DNA; the coding
DNA sequence without introns made using RT from
mRNA
BLAT - answer (BLAST-like alignment tool) BLAT
parses an entire
genomic DNA database into words (11 k-mers),
then
searches them against a query. Thus it is a mirror
image
of the BLAST strategy. It is designed to quickly
find DNA sequences of 95% and greater similarity
of length 25 bases or more. It may miss more
divergent or shorter sequence alignments.
gene coordinate - answer chromosome start-stop
UCSC genes track - answer set of gene predictions
based on data from RefSeq, GenBank, CCDS, Rfam,
and the tRNA Genes track. It includes both protein-
coding genes and non-coding RNA genes.
systems biology - answer study of an organism,
viewed as integrated and interacting networks of
,genes, proteins and biochemical reactions which
give rise to life
genome - answer DNA sequences of all
chromosomes of an organism
bioinformatics - answer technology that uses
computers for storage, retrieval, manipulation, and
distribution of information related to biological
macromolecules (DNA, RNA, proteins, metabolites,
and lipids).
It is at the interface of biological measurement and
result
2 bioinformatics subfields - answer Development of
computational tools and databases
Application of those tools to biological problems
3 basic areas of bioinformatics research - answer
molecular sequence, structure, and function
analysis
sequence analysis - answer genome comparison,
phylogeny, gene and promoter prediction, motif
discovery, sequence database searching, sequence
alignment
, structure analysis - answer nucleic acid structure
prediction, protein structure prediction,
classification, and comparison
function analysis - answer metabolic pathway
modeling, gene expression profiling, protein
interaction prediction, protein subcellular
localization prediction
computational biology - answer Theoretical
biological model building and simulation.
database - answer digital archive used to store and
organize data (logical info organization=schema) in
such a way that information can be retrieved easily
using a variety of search criteria
biological database - answer library of life sciences
information, collected from scientific experiments,
published literature, high throughput experiment
technology, and computational analyses. They
contain information from research areas including
genomics, proteomics, metabolomics, microarray
gene expression, and phylogenetics. Information
contained in biological databases includes gene
function, structure, localization (both cellular and
chromosomal), clinical effects of mutations as well
as similarities of biological sequences and
structures.
