春日部来的

DNA sequencing as initially valued for revealing the DNA content of a cell. It may come as a surprise to many, however, that the most significant promise for the future of bioinformatics might lie in other applications. In general, most bioinformatics problems fall under one of four categories:

1. Classification: determining the species composition of a population of organisms

2. Assembly: establishing the nucleotide composition of genomes

3. Resequencing: identifying mutations and variations in genomes

4. Quantification: using DNA sequencing to measure the functional characteristics of a cell

The Human Genome Project fell squarely in the assembly category. Since its completion, scientists have assembled the genomes of thousands of others species. The genomes of many millions of species, however, remain entirely unknown.

Studies that attempt to identify changes relative to known genomes fall into the resequencing field of study. DNA mutations and variants may cause phenotypic changes like emerging diseases, changing fitness, different survival rates, and many others. For example, there are several ongoing efforts to compile all variants present in the human genome—-these efforts would fall into the resequencing category. Thanks to the work of bioinformaticians, massive computing efforts are underway to produce clinically valuable information from the knowledge gained through resequencing.

Living micro-organisms surround us, and we coexist with them in complex collectives that can only survive by maintaining interdependent harmony. Classifying these mostly-unknown species of micro-organisms by their genetic material is a fast-growing subfield of bioinformatics.

Finally, and perhaps most unexpectedly, bioinformatics methods can help us better understand biological processes, like gene expressions, through quantification. In these protocols, the sequencing procedures are used to determine the relative abundances of various DNA fragments that were made to correlate with other biological processes.

Over the decades biologists have become experts at manipulating DNA and are now able to co-opt the many naturally-occurring molecular processes to copy, translate, and reproduce DNA molecules and connect these actions to biological processes. Sequencing has opened a new window into this world, new methods and sequence manipulations are continuously discovered. The various methods are typically named as Something-Seq for example RNA-Seq, Chip-Seq, RAD-Seq to reflect what mechanism was captured/connected to sequencing. For example, RNA-Seq reveals the abundance of RNA by turning it into DNA via reverse transcription. Sequencing this construct allows for simultaneously measuring the expression levels of all genes of a cell. The for example RAD-Seq uses restriction enzymes to cleave DNA at specific locations and only the fragments around these locations are then sequenced. This method produces very high coverage around these sites, thus is suited for population genetics studies.