Biology Reference
In-Depth Information
The amount of data produced from genomics is stressing the system (
Kahn
2011
). A single week-long sequencing run can produce as much data as did
entire genome centers a few years ago. Thus, the availability of large genomic
data sets raises concerns over access to the data and its security. “A doubling
of sequencing output every nine months has outpaced and overtaken perfor-
mance improvements within the disk storage and high-performance computa-
tion fields” (
Kahn 2011
).
Improvements in analysis methods are ongoing. The
modENCODE Consortium
(2010)
involves projects to map transcripts, histone modifications, chromosomal
proteins, transcription factors, replication proteins, and nucleosome properties
across a developmental time course and in multiple cell lines, tripling the anno-
tated portion of the
Drosophila
genome.
Fan and Li (2012)
reported the results
of comparisons of eight genome assemblers.
Zerbino et al. (2012)
report on the
development of models from population genetics and phylogenetics and their
relationship with graph theory, statistics, signal processing, and computer sci-
ence to “provide a rich quantitative foundation for genomics that can only be
realized with the aid of a computer.”
7.12.1 Gene Ontology
Gene Ontology (GO) is a bioinformatics project with the goal of standardizing
the representation of gene and gene-product attributes across species and data-
bases. The goal is to provide a specific vocabulary of terms for describing gene
product and gene-product annotation data, as well as to provide tools to access
and process the data (
www.geneontology.org
)
. The goal is to “unify” biol-
ogy, so that different scientists use the same terms and references to function
(
Ashburner et al. 2000, Gene Ontology Consortium 2001
). The ontology is set
up with three sets of terms to describe molecular function, biological process,
and cellular component. The model organisms (human, yeast and
Drosophila
)
were annotated using GO terms, and this has become the standard for other
genomes. The GO website provides access to the annotated gene-product data
sets. It should be remembered, however, that
sequence similarity does not nec-
essarily equate to similar functions
. Until the function of a gene has been evalu-
ated in a particular species, the assigned function is “putative.”
7.13 Genome Analyses of Other Arthropods
The ability to sequence the
Drosophila
genome led to proposals to sequence the
genomes of other arthropods, especially species that are of significant economic
importance such as mosquitoes (
Anopheles gambiae
, the vector of malaria) and
