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Emmanuel Sitnikov
Emmanuel Sitnikov

Bioinformatics For Beginners : Genes, Genomes, ... PATCHED

Research in Bioinformatics and Genomics at UVA uses quantitative methods to describe the behavior of genes, genomes, and biological systems.At the intersection of experimental and computational biology, genomics research involves interpretation and integration of large-scale, genome-wide datasets.

Bioinformatics for beginners : genes, genomes, ...

In this review, we survey several of the most interesting computational problems that arise from WGS sequencing of communities. Traditional approaches to classic bioinformatics problems such as assembly, gene finding, and phylogeny need to be reconsidered in light of this new kind of data, while new problems need to be addressed, including how to compare communities, how to separate sequence from different organisms in silico, and how to model population structures using WGS assembly statistics. We discuss all these problems and their connections to other areas of bioinformatics, such as the assembly of highly polymorphic genomes, gene expression analysis, and supertree methods for phylogenetic reconstruction.

The number of new community shotgun sequencing projects continues to grow, promising to provide vast quantities of sequence data for analysis. Samples are being drawn from macroscopic environments such as the sea and air, as well as from more contained communities such as the human mouth (Table 3). Exciting advances in our understanding of ecosystems, environments, and communities will require creative solutions to numerous new bioinformatics problems. We have briefly mentioned some of these: assembly (can co-assembly techniques be used to assemble polymorphic genomes and complex communities?), binning (what is the best way to combine diverse sources of information to bin scaffolds?), gene finding (how should gene finding programs, which were designed for complete genes and genomes, be adapted for low-coverage sequence?), fingerprinting (which clustering techniques are best suited for discovering novel pathways and functional groups that allow communities to adapt to their environments?), and MSA and phylogeny (how can we best construct trees and alignments from fragmented data?). 041b061a72


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