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共370条结果
  • 1.

    【2hr】FSH: fast spaced seed hashing exploiting adjacent hashes

    包量

    机译 FSH：利用相邻散列的快速间隔种子哈希
    摘要：BackgroundPatterns with wildcards in specified positions, namely spaced seeds, are increasingly used instead of k-mers in many bioinformatics applications that require indexing, querying and rapid similarity search, as they can provide better sensitivity. Many of these applications require to compute the hashing of each position in the input sequences with respect to the given spaced seed, or to multiple spaced seeds. While the hashing of k-mers can be rapidly computed by exploiting the large overlap between consecutive k-mers, spaced seeds hashing is usually computed from scratch for each position in the input sequence, thus resulting in slower processing.
  • 2.

    【2hr】Finding local genome rearrangements

    包量

    机译 寻找局部基因组重排
    摘要：BackgroundThe double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been devoted to the understanding of minimum length scenarios transforming one genome into another. In this paper we search instead for rearrangement scenarios that minimize the number of rearrangements whose breakpoints are unlikely due to some biological criteria. One such criterion has recently become accessible due to the advent of the Hi-C experiment, facilitating the study of 3D spacial distance between breakpoint regions.
  • 3.

    【2hr】A fast and accurate enumeration-based algorithm for haplotyping a triploid individual

    包量

    机译 一种快速准确的基于枚举的三倍体个体单倍型算法
    摘要：BackgroundHaplotype assembly, reconstructing haplotypes from sequence data, is one of the major computational problems in bioinformatics. Most of the current methodologies for haplotype assembly are designed for diploid individuals. In recent years, genomes having more than two sets of homologous chromosomes have attracted many research groups that are interested in the genomics of disease, phylogenetics, botany and evolution. However, there is still a lack of methods for reconstructing polyploid haplotypes.
  • 4.

    【2hr】Locus-aware decomposition of gene trees with respect to polytomous species trees

    包量

    机译 基因树相对于多物种树的基因座感知分解
    摘要：BackgroundHorizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most of them either rely on approximate, non-phylogenetic methods or on the tree reconciliation, which is computationally intensive and sensitive to parameter values.
  • 5.

    【2hr】Split-inducing indels in phylogenomic analysis

    包量

    机译 分裂诱导的插入缺失
    摘要：BackgroundMost phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps.
  • 6.

    【2hr】Sorting signed circular permutations by super short operations

    包量

    机译 通过超短运算对有符号循环排列进行排序
    摘要：BackgroundOne way to estimate the evolutionary distance between two given genomes is to determine the minimum number of large-scale mutations, or genome rearrangements, that are necessary to transform one into the other. In this context, genomes can be represented as ordered sequences of genes, each gene being represented by a signed integer. If no gene is repeated, genomes are thus modeled as signed permutations of the form π = (π1π2…πn), and in that case we can consider without loss of generality that one of them is the identity permutation ιn = (12…n), and that we just need to sort the other (i.e., transform it into ιn). The most studied genome rearrangement events are reversals, where a segment of the genome is reversed and reincorporated at the same location; and transpositions, where two consecutive segments are exchanged. Many variants, e.g., combining different types of (possibly constrained) rearrangements, have been proposed in the literature. One of them considers that the number of genes involved, in a reversal or a transposition, is never greater than two, which is known as the problem of sorting by super short operations (or SSOs).
  • 7.

    【2hr】Improved de novo peptide sequencing using LC retention time information

    包量

    机译 使用LC保留时间信息改进了从头肽测序
    摘要：BackgroundLiquid chromatography combined with tandem mass spectrometry is an important tool in proteomics for peptide identification. Liquid chromatography temporally separates the peptides in a sample. The peptides that elute one after another are analyzed via tandem mass spectrometry by measuring the mass-to-charge ratio of a peptide and its fragments. De novo peptide sequencing is the problem of reconstructing the amino acid sequences of a peptide from this measurement data. Past de novo sequencing algorithms solely consider the mass spectrum of the fragments for reconstructing a sequence.
  • 8.

    【2hr】Coordinate systems for supergenomes

    包量

    机译 超级基因组的坐标系
    摘要：BackgroundGenome sequences and genome annotation data have become available at ever increasing rates in response to the rapid progress in sequencing technologies. As a consequence the demand for methods supporting comparative, evolutionary analysis is also growing. In particular, efficient tools to visualize-omics data simultaneously for multiple species are sorely lacking. A first and crucial step in this direction is the construction of a common coordinate system. Since genomes not only differ by rearrangements but also by large insertions, deletions, and duplications, the use of a single reference genome is insufficient, in particular when the number of species becomes large.
  • 9.

    【2hr】Superbubbles revisited

    包量

    机译 重温超级泡沫
    摘要：BackgroundSuperbubbles are distinctive subgraphs in direct graphs that play an important role in assembly algorithms for high-throughput sequencing (HTS) data. Their practical importance derives from the fact they are connected to their host graph by a single entrance and a single exit vertex, thus allowing them to be handled independently. Efficient algorithms for the enumeration of superbubbles are therefore of important for the processing of HTS data. Superbubbles can be identified within the strongly connected components of the input digraph after transforming them into directed acyclic graphs. The algorithm by Sung et al. (IEEE ACM Trans Comput Biol Bioinform 12:770–777, ) achieves this task in O(mlog(m))-time. The extraction of superbubbles from the transformed components was later improved to by Brankovic et al. (Theor Comput Sci 609:374–383, ) resulting in an overall O(m+n)-time algorithm.
  • 10.

    【2hr】Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments

    包量

    机译 Regmex：一种统计工具，用于从基因组学实验中探索排名序列表中的基序
    摘要：BackgroundMotif analysis methods have long been central for studying biological function of nucleotide sequences. Functional genomics experiments extend their potential. They typically generate sequence lists ranked by an experimentally acquired functional property such as gene expression or protein binding affinity. Current motif discovery tools suffer from limitations in searching large motif spaces, and thus more complex motifs may not be included. There is thus a need for motif analysis methods that are tailored for analyzing specific complex motifs motivated by biological questions and hypotheses rather than acting as a screen based motif finding tool.
  • 11.

    【2hr】Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds

    包量

    机译 11110110111的热门精选：无种子种子的无模型选择和无参数灵敏度计算
    • 作者：Laurent Noé
    • 刊名：Algorithms for Molecular Biology : AMB
    • 2017年第期
    摘要：Background Spaced seeds, also named gapped q-grams, gapped k-mers, spaced q-grams, have been proven to be more sensitive than contiguous seeds (contiguous q-grams, contiguous k-mers) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities and to anchor sequence alignments, spaced seeds have more recently been applied in several alignment-free related methods. Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates. Moreover, it can be altered by a set of arbitrary chosen parameters from the probabilistic alignment models used. In this general context, Dominant seeds have been introduced by Mak and Benson (Bioinformatics 25:302–308, 2009) on the Bernoulli model, in order to reduce the number of spaced seed candidates that are further processed in a parameter-free calculation of the sensitivity.
  • 12.

    【2hr】Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

    包量

    机译 在短RNA-seq读段的局部和全局从头转录组中重复进行捉迷藏
    摘要：Background The main challenge in de novo genome assembly of DNA-seq data is certainly to deal with repeats that are longer than the reads. In de novo transcriptome assembly of RNA-seq reads, on the other hand, this problem has been underestimated so far. Even though we have fewer and shorter repeated sequences in transcriptomics, they do create ambiguities and confuse assemblers if not addressed properly. Most transcriptome assemblers of short reads are based on de Bruijn graphs (DBG) and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them.
  • 13.

    【2hr】Approximating the DCJ distance of balanced genomes in linear time

    包量

    机译 在线性时间内近似平衡基因组的DCJ距离
    摘要：BackgroundRearrangements are large-scale mutations in genomes, responsible for complex changes and structural variations. Most rearrangements that modify the organization of a genome can be represented by the double cut and join (DCJ) operation. Given two balanced genomes, i.e., two genomes that have exactly the same number of occurrences of each gene in each genome, we are interested in the problem of computing the rearrangement distance between them, i.e., finding the minimum number of DCJ operations that transform one genome into the other. This problem is known to be NP-hard.
  • 14.

    【2hr】Approximating the correction of weighted and unweighted orthology and paralogy relations

    包量

    机译 近似校正加权和未加权的正字和副词之间的关系
    摘要：BackgroundGiven a gene family, the relations between genes (orthology/paralogy), are represented by a relation graph, where edges connect pairs of orthologous genes and “missing” edges represent paralogs. While a gene tree directly induces a relation graph, the converse is not always true. Indeed, a relation graph is not necessarily “satisfiable”, i.e. does not necessarily correspond to a gene tree. And even if that holds, it may not be “consistent”, i.e. the tree may not represent a true history in agreement with a species tree. Previous studies have addressed the problem of correcting a relation graph for satisfiability and consistency. Here we consider the weighted version of the problem, where a degree of confidence is assigned to each orthology or paralogy relation. We also consider a maximization variant of the unweighted version of the problem.
  • 15.

    【2hr】On avoided words, absent words, and their application to biological sequence analysis

    包量

    机译 关于避免词，缺词及其在生物序列分析中的应用
    摘要：Background The deviation of the observed frequency of a word w from its expected frequency in a given sequence x is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of the deviation of w, denoted by dev(w), effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word w of length k > 2 is a ρ-avoided word in x if dev(w) ≤ ρ, for a given threshold ρ < 0. Notice that such a word may be completely absent from x. Hence, computing all such words naïvely can be a very time-consuming procedure, in particular for large k.
  • 16.

    【2hr】On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model

    包量

    机译 复制损失合并模型中最大简约对账问题的计算复杂度
    摘要：BackgroundPhylogenetic tree reconciliation is a widely-used method for inferring the evolutionary histories of genes and species. In the duplication-loss-coalescence (DLC) model, we seek a reconciliation that explains the incongruence between a gene and species tree using gene duplication, loss, and deep coalescence events. In the maximum parsimony framework, costs are associated with these event types and a reconciliation is sought that minimizes the total cost of the events required to map the gene tree onto the species tree.
  • 17.

    【2hr】An efficient algorithm for testing the compatibility of phylogenies with nested taxa

    包量

    机译 一种测试系统发育与巢状类群相容性的有效算法
    摘要：
  • 18.

    【2hr】Gerbil: a fast and memory-efficient k-mer counter with GPU-support

    包量

    机译 Gerbil：具有GPU支持的快速且高效存储的k-mer计数器
    摘要：BackgroundA basic task in bioinformatics is the counting of k-mers in genome sequences. Existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degrading performance for large k. However, given the technology trend towards long reads of next-generation sequencers, support for large k becomes increasingly important.
  • 19.

    【2hr】Aligning coding sequences with frameshift extension penalties

    包量

    机译 将编码序列与移码扩展罚分进行比对
    摘要：BackgroundFrameshift translation is an important phenomenon that contributes to the appearance of novel coding DNA sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of gene coding regions. Frameshift translations can be identified by aligning two CDS, from a same gene or from homologous genes, while accounting for their codon structure. Two main classes of algorithms have been proposed to solve the problem of aligning CDS, either by amino acid sequence alignment back-translation, or by simultaneously accounting for the nucleotide and amino acid levels. The former does not allow to account for frameshift translations and up to now, the latter exclusively accounts for frameshift translation initiation, not considering the length of the translation disruption caused by a frameshift.
  • 20.

    【2hr】Core column prediction for protein multiple sequence alignments

    包量

    机译 蛋白质多序列比对的核心柱预测
    摘要：BackgroundIn a computed protein multiple sequence alignment, the coreness of a column is the fraction of its substitutions that are in so-called core columns of the gold-standard reference alignment of its proteins. In benchmark suites of protein reference alignments, the core columns of the reference alignment are those that can be confidently labeled as correct, usually due to all residues in the column being sufficiently close in the spatial superposition of the known three-dimensional structures of the proteins. Typically the accuracy of a protein multiple sequence alignment that has been computed for a benchmark is only measured with respect to the core columns of the reference alignment. When computing an alignment in practice, however, a reference alignment is not known, so the coreness of its columns can only be predicted.
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