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Major Research Areas Sequence analysis
Since the Phage Φ-X174 was sequenced in 1977, the DNA sequences of hundreds of organisms have been decoded and stored in databases. These data are analyzed to determine genes that code for proteins, as well as regulatory sequences. A comparison of genes within a species or between different species can show similarities between protein functions, or relations between species (the use of molecular systematics to construct phylogenetic trees). With the growing amount of data, it long ago became impractical to analyze DNA sequences manually. Today, computer programs are used to search the genome of thousands of organisms, containing billions of nucleotides. These programs can compensate for mutations (exchanged, deleted or inserted bases) in the DNA sequence, in order to identify sequences that are related, but not identical. A variant of this sequence alignment is used in the sequencing process itself. The so-called shotgun sequencing technique (which was used, for example, by The Institute for Genomic Research to sequence the first bacterial genome, Haemophilus influenza) does not give a sequential list of nucleotides, but instead the sequences of thousands of small DNA fragments (each about 600-800 nucleotides long). The ends of these fragments overlap and, when aligned in the right way, make up the complete genome. Shotgun sequencing yields sequence data quickly, but the task of assembling the fragments can be quite complicated for larger genomes. In the case of the Human Genome Project, it took several months of CPU time (on a circa-2000 vintage DEC Alpha computer) to assemble the fragments. Shotgun sequencing is the method of choice for virtually all genomes sequenced today, and genome assembly algorithms are a critical area of bioinformatics research.
Another aspect of bioinformatics in sequence analysis is the automatic search for genes and regulatory sequences within a genome. Not all of the nucleotides within a genome are genes. Within the genome of higher organisms, large parts of the DNA do not serve any obvious purpose. This so-called junk DNA may, however, contain unrecognized functional elements. Bioinformatics helps to bridge the gap between genome and proteome projects--for example, in the use of DNA sequences for protein identification.
Genome annotation
In the context of genomics, annotation is the process of marking the genes and other biological features in a DNA sequence. The first genome annotation software system was designed in 1995 by Owen White, who was part of the team that sequenced and analyzed the first genome of a free-living organism to be decoded, the bacterium Haemophilus influenzae. Dr. White built a software system to find the genes (places in the DNA sequence that encode a protein), the transfer RNA, and other features, and to make initial assignments of function to those genes. Most current genome annotation systems work similarly, but the programs available for analysis of genomic DNA are constantly changing and improving.
Computational evolutionary biology
Evolutionary biology is the study of the origin and descent of species, as well as their change over time. Informatics has assisted evolutionary biologists in several key ways; it has enabled researchers to:
• trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone, • more recently, compare entire genomes, which permits the study of more complex evolutionary events, such as gene duplication, lateral gene transfer, and the prediction of bacterial speciation factors, • build complex computational models of populations to predict the outcome of the system over time • track and share information on an increasingly large number of species and organisms
Future work endeavours to reconstruct the now more complex tree of life.
The area of research within computer science that uses genetic algorithms is sometimes confused with computational evolutionary biology, but the two areas are unrelated.
Measuring biodiversity
Biodiversity of an ecosystem might be defined as the total genomic complement of a particular environment, from all of the species present, whether it is a biofilm in an abandoned mine, a drop of sea water, a scoop of soil, or the entire biosphere of the planet Earth. Databases are used to collect the species names, descriptions, distributions, genetic information, status and size of populations, habitat needs, and how each organism interacts with other species. Specialized software programs are used to find, visualize, and analyze the information, and most importantly, communicate it to other people. Computer simulations model such things as population dynamics, or calculate the cumulative genetic health of a breeding pool (in agriculture) or endangered population (in conservation). One very exciting potential of this field is that entire DNA sequences, or genomes of endangered species can be preserved, allowing the results of Nature's genetic experiment to be remembered in silico, and possibly reused in the future, even if that species is eventually lost.
Important Projects: Species 2000 project.
Major Research Areas Sequence analysis Prediction of protein structure
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