We study the shotgun assembly problem for lattice labeling model, where i.i.d. uniform labels are assigned to each vertex in a d-dimensional box of side length n. wish recover configuration on whole given empirical profile configurations all boxes r. determine threshold around which there is sharp transition from impossible with probability tending 1, possible an efficient algorithm 1. Our resu...

Graph shotgun assembly refers to the problem of reconstructing a graph from collection local neighborhoods. In this paper, we consider Erdős–Rényi random graphs G(n,pn), where pn=n−α for 0<α<1. We both reconstruction up isomorphism as well exact (recovering vertex labels structure). show that given distance-1 neighborhoods, G is exactly reconstructable 0<α<1 3, but not 1 2<α<1. Given distance-2...

Hierarchical genome assembly can be divided into three distinct stages: sequencing and assembling shotgun reads for each of a series of selected BAC clones; assembling the resulting fragments into BAC consensus sequences; and mapping and orienting the BAC consensus according to external positional information. We report a new approach for BAC consensus assembly that relies on iterative layouts ...

The large amount of repeats, especially high copy repeats, in the genomes of higher animals and plants makes whole genome assembly (WGA) quite difficult. In order to solve this problem, we tried to identify repeats and mask them prior to assembly even at the stage of genome survey. It is known that repeats of different copy number have different probabilities of appearance in shotgun data, so b...

Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge diversity distribution methane-oxidizing bacteria (MOB) or methanogens in karst caves sub-surface environment general. Here, we performed survey 14 shotgun metagenomes from cave covering broad set environmental con...

Most large-scale genome sequencing projects use the whole-genome shotgun sequencing strategy, in which a genome is shattered into numerous small fragments and the fragments are then sequenced from both ends. The resulting sequences (called fragments or reads) must then be assembled to reconstruct the chromosomes of the genome. Current technology produces reads of length 600-800 base pairs (bp) ...

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning , to make large metagenome assembl...