phylogenetic comparative assembly系统发育比较大会.pdf

Husemann and Stoye Algorithms for Molecular Biology 2010, 5:3 /content/5/1/3 RESEARCH Open Access Phylogenetic comparative assembly Peter Husemann1,2*, Jens Stoye1,3 Abstract Background: Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. Results: Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a graph that contains the likelihood for each pair of contigs to be adjacent. Subsequently, this graph can be used to compute a layout graph that shows the most promising contig adjacen- cies in order to aid biologists in finishing the complete genomic sequence. The layout graph shows unique contig orderings where possible, and the best alternatives where necessary. Conclusions: Our new algorithm for contig ordering uses sequence similarity as well as phylogenetic information to estimate adjacencies of contigs. An evaluation of our implementation shows that it performs better than recent approaches while being much faster at the same time. Background sequencing [5]. These PCRs ideally run towards each Today the nucleotide sequences of many genomes are other until the sequences overlap. To close a gap com- known. In the first genome projects, the process of pletely, new primer pairs have to be generated again and obtaining the DNA sequence by multi-step clone-by- again since