Finally we show that besides the smaller size of a minimum SPSS, it also has advantages in downstream applications. As an example of ak-mer-based method, we query our compressed representation with the tools SSHash [45] and Bifrost [23]. These are state-of-the-art tools supportingk-mer-...
Initial analysis using only densely populatedk-mer databases performed well. However, despite being on average over an order of magnitude smaller than the input sequence database size (see below), we determined that loading the entire densely merged “tree_filter.dbs” into memory for analysis un...
The speedup of these tech- niques is traded in for a loss of accuracy, compared to the alignment-based methods. Nevertheless, it has been shown that k-mer profiles are distinctive enough for bin- ning in metagenomic studies and for classification up to certain levels in the tree of life [...
I here provide a data structure with strong similarities to the FM-index, but which stores the de Bruijn subgraph representing thek-mer substrings rather than entire sequences. It is based on the idea of storing for each vertex which of the possible in-coming edges are actually present. For...
Traditionally, occurrence counts fork-mers are computed by hashing methods. However, these only work, if the number 4kof possiblek-mers is considerably smaller thann. This does not hold for our application, wherekranges from 10 to 500. We have developed a different approach based on enhanced ...
This construction algorithm is based on the lightning-fastk-mer counter KMC. We call the KMC binaries directly from our code. The construction is very disk-heavy, so it is recommended to run construction code off a fast SSD drive.
Fig. 1. NJ phylogenetic tree of beta-globin protein sequence of 88 species based on the k-mer natural vector method. The 88 beta-globin sequences are correctly clustered into 20 groups: Carnivora, Primates, Sirenia, Insectivora, Perissodactyla, Hyracoidea, Proboscidea, Rodentia, Diprotodontia,...
The speedup of these techniques is traded in for a loss of accuracy, compared to the alignment-based methods. Nevertheless, it has been shown that k-mer profiles are distinctive enough for binning in metagenomic studies and for classification up to certain levels in the tree of life [21]. ...
Construction of phylogenetic tree based on DNA sequences; 基于DNA序列的系统进化树构建 3. Approach to propreties of coding and non-coding DNA sequence based on complex network theory; 基于网络方法的DNA序列编码区·非编码区性质研究 更多例句>> 4...