作者: gonioscopy 時間: 2025-3-21 20:56
Domain Architecture in Homolog Identification,of mis-assignments due to the alignment of homologous domains in otherwise unrelated sequences. Here we propose methods to detect homologs through explicit comparison of domain architecture. We developed several schemes for scoring the similarity of a pair of protein sequences by exploiting an analo作者: 披肩 時間: 2025-3-22 00:59 作者: 山頂可休息 時間: 2025-3-22 06:16 作者: HAVOC 時間: 2025-3-22 12:06 作者: lanugo 時間: 2025-3-22 16:06 作者: lanugo 時間: 2025-3-22 20:56 作者: AUGUR 時間: 2025-3-22 21:33
Sorting by Translocations Via Reversals Theory,shortest sequence of genome rearrangements that “sorts” one genome into another. In this paper we focus on sorting a multi-chromosomal genome by translocations. We reveal new relationships between this problem and the well studied problem of sorting by reversals. Based on these relationships, we dev作者: macabre 時間: 2025-3-23 02:17
Inferring Gene Orders from Gene Maps Using the Breakpoint Distance,ing techniques usually give rise to different maps with unequal gene content, and often containing sets of unordered neighboring genes. Only partial orders can thus be obtained from combining such maps. However, once a total order . is known for a given genome, it can be used as a reference to order作者: GEST 時間: 2025-3-23 07:24
Ordering Partially Assembled Genomes Using Gene Arrangements, the problem of ordering the contigs of two partially assembled genomes so as to maximize the similarity (measured in terms of genome rearrangements) between the assembled genomes. We give a linear-time algorithm for the .: Given two signed permutations (genomes) that are been broken into blocks (co作者: alcoholism 時間: 2025-3-23 11:22 作者: 溫和女孩 時間: 2025-3-23 16:24
A PQ Framework for Reconstructions of Common Ancestors and Phylogeny,versions and transpositions within the members of the species have also been made over the years. The task of constructing a phylogeny tree of the members of the same species, given this knowledge and data, is an important problem. In this context, a key observation is that the “distance” between tw作者: Heterodoxy 時間: 2025-3-23 21:59
Intron Loss Dynamics in Mammals, mammalian genes. We found no evidence for intron gain and 122 cases of intron loss, most of which occurred within the rodent lineage. Majority (68%) of the deleted introns were extremely small (<150 bp), significantly smaller than average. The intron losses occurred almost exclusively within highly作者: Offensive 時間: 2025-3-23 22:56
Finding Maximum Likelihood Indel Scenarios,most likely scenario of insertions and deletions capable of explaining the gaps observed in the alignment. This problem, that we called the Indel Maximum Likelihood Problem (IMLP), is an important step toward the reconstruction of ancestral genomics sequences, and is important for studying evolution作者: byline 時間: 2025-3-24 05:40
Conservation Patterns in ,-Elements Reveal Compensatory Mutations,nts. A better understanding and modelling of the TF-DNA interaction is an important area of research. The Positional Weight Matrix (PWM) is the most common model of TF-DNA binding and it presumes that the nucleotide preferences at individual positions within the binding site are independent. However作者: 不知疲倦 時間: 2025-3-24 07:41
Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-y been partially addressed in prokaryotes and lower eukaryotes. Given the higher length of regulatory regions and the relative low complexity of DNA binding signature, however, methods to address this problem in higher order eukaryotes are lacking. In this paper, we propose a novel computational fra作者: 單片眼鏡 時間: 2025-3-24 12:31
Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer,ificance on understanding prokaryotic genome diversification and unraveling their complexities. Phylogeny-based detection of HGT is one of the most commonly used approaches for this task, and is based on the fundamental fact that HGT may cause gene trees to disagree with one another, as well as with作者: AUGUR 時間: 2025-3-24 17:35 作者: BACLE 時間: 2025-3-24 21:40
Software Engineering and Environmentw that dependent positions are more likely to be functional, as evidenced by a higher information content and higher conservation. We discuss two examples—Elk-1 and SAP-1 where the inferred compensatory mutation is consistent with known TF-DNA crystal structure.作者: diskitis 時間: 2025-3-24 23:59 作者: inflame 時間: 2025-3-25 05:10 作者: Coterminous 時間: 2025-3-25 11:31
How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation,phasis on common intervals under the maximum matching model. Of particular importance, we show very strong evidence that the simple LCS heuristic provides very good results on a well-known public benchmark dataset of .-Proteobacteria.作者: painkillers 時間: 2025-3-25 15:04
Conservation Patterns in ,-Elements Reveal Compensatory Mutations,w that dependent positions are more likely to be functional, as evidenced by a higher information content and higher conservation. We discuss two examples—Elk-1 and SAP-1 where the inferred compensatory mutation is consistent with known TF-DNA crystal structure.作者: dermatomyositis 時間: 2025-3-25 19:33 作者: 擁護者 時間: 2025-3-25 20:52 作者: 沖擊力 時間: 2025-3-26 01:28
Social Protection in Latin Americaroblem in the space (2.,.) as the basis for constructing phylogenetic trees, including ancestral gene orders. We extend this to genomes with unequal gene content and to genomes containing gene families. Applied to streptophyte phylogeny, our method does not support the positioning of the complex algae . as a sister group to the land plants.作者: Liability 時間: 2025-3-26 07:52 作者: 拒絕 時間: 2025-3-26 11:03 作者: Excitotoxin 時間: 2025-3-26 16:29
Shunsuke Iwata,Katsuhiro Honda,Akira Notsuucture (termed oPQ) and show that both the number and size of each . is .. We further show that the tree reconstruction problem is statistically well-defined (Theorem [7]) and give a simple scheme to construct the phylogeny tree and the common ancestors. Our preliminary experiments with simulated data look very promising.作者: 愛哭 時間: 2025-3-26 20:35
https://doi.org/10.1007/978-1-4615-5907-8ce the most likely ancestral reconstruction and to compute the level of confidence associated to specific regions of the reconstruction. The method is illustrated on a set of 85kb sequences from eight mammals.作者: 肉體 時間: 2025-3-26 21:50 作者: FLIT 時間: 2025-3-27 04:54 作者: bronchiole 時間: 2025-3-27 07:55 作者: 影響 時間: 2025-3-27 10:52 作者: ABIDE 時間: 2025-3-27 13:49
https://doi.org/10.1007/978-3-658-19455-0mes using the minimum number of common intervals is .-complete and we give a simple heuristic for this problem. We illustrate the effectiveness of this first approach using common intervals of sequences on two datasets, respectively 8 .-proteobacterial genomes and the human and mouse whole genomes.作者: 藕床生厭倦 時間: 2025-3-27 20:16 作者: chassis 時間: 2025-3-27 23:29
Sociological Perspectives on Labor Marketsd. We illustrate our algorithm on a set of 90 markers from the human and mouse chromosomes X and show how the size of the contigs and the rearrangement distance between the two genomes affects the accuracy of the predicted assemblies. The appendix and an implementation are available at ..作者: Jubilation 時間: 2025-3-28 06:07 作者: 并排上下 時間: 2025-3-28 07:58
Inferring Positional Homologs with Common Intervals of Sequences,mes using the minimum number of common intervals is .-complete and we give a simple heuristic for this problem. We illustrate the effectiveness of this first approach using common intervals of sequences on two datasets, respectively 8 .-proteobacterial genomes and the human and mouse whole genomes.作者: 原來 時間: 2025-3-28 14:21
Sorting by Translocations Via Reversals Theory,n’s algorithm, and a recursive procedure similar to the Berman-Hannenhalli method. Though their proofs are more involved, our procedures for translocations match the complexities of the original ones for reversals.作者: forbid 時間: 2025-3-28 16:20 作者: FILLY 時間: 2025-3-28 19:26 作者: Defiance 時間: 2025-3-29 00:15
Intron Loss Dynamics in Mammals, expressed, housekeeping genes, supporting the hypothesis that intron loss is mediated via germline recombination with spliced mRNA intermediates. This study constitutes the largest scale analysis for intron dynamics in vertebrates to date and allows us to confirm and extend several hypotheses previously based on much smaller samples.作者: 集聚成團 時間: 2025-3-29 05:09
https://doi.org/10.1007/978-3-658-19455-0ribution of gene families. The formulas for equilibrium gene family sizes are derived showing that they follow a logarithmic distribution. We consider also a disjoint union of DLCI models and we present the result of this study. Some empirical results for microbial genomes are presented.作者: Expostulate 時間: 2025-3-29 07:21 作者: 都相信我的話 時間: 2025-3-29 14:50
Sociological Perspectives on Labor Marketsrepeated genes. We present a time-efficient branch-and-bound algorithm and show, using simulated data, that it can be used to detect “wrong” phylogenies among a set of putative ones for a given gene family. An application on a published phylogeny of KRAB zinc finger genes is presented.作者: 裂隙 時間: 2025-3-29 16:26
On Genome Evolution with Accumulated Change and Innovation,ribution of gene families. The formulas for equilibrium gene family sizes are derived showing that they follow a logarithmic distribution. We consider also a disjoint union of DLCI models and we present the result of this study. Some empirical results for microbial genomes are presented.作者: 你敢命令 時間: 2025-3-29 22:30
Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes,es of length . and . chromosomes, we show that the expectation of . + .– . is .. We then discuss how to extend these analyses to the case where intra- and interchromosomal operations have different probabilities.作者: 鎮(zhèn)壓 時間: 2025-3-30 01:25
Evolution of Tandemly Repeated Sequences Through Duplication and Inversion,repeated genes. We present a time-efficient branch-and-bound algorithm and show, using simulated data, that it can be used to detect “wrong” phylogenies among a set of putative ones for a given gene family. An application on a published phylogeny of KRAB zinc finger genes is presented.作者: Anticoagulants 時間: 2025-3-30 07:47
Reconstructing Domain Compositions of Ancestral Multi-domain Proteins,ins. Given a set of contemporary multidomain proteins from different species together with a species tree, in this paper, we suggest a model for constructing the domain compositions of ancestral multi-domain proteins considering the above evolutionary events.作者: Entreaty 時間: 2025-3-30 11:48
https://doi.org/10.1007/11864127Alignment; DNA sequences; comparative genomics; comparative maps; complexity; computational genomics; copu作者: 變形詞 時間: 2025-3-30 15:37 作者: 在前面 時間: 2025-3-30 20:16
Lecture Notes in Computer Sciencehttp://image.papertrans.cn/c/image/230903.jpg作者: anaphylaxis 時間: 2025-3-30 21:27 作者: 朦朧 時間: 2025-3-31 04:03
https://doi.org/10.1007/978-94-009-8162-1of mis-assignments due to the alignment of homologous domains in otherwise unrelated sequences. Here we propose methods to detect homologs through explicit comparison of domain architecture. We developed several schemes for scoring the similarity of a pair of protein sequences by exploiting an analo作者: Carcinogen 時間: 2025-3-31 07:34 作者: 最小 時間: 2025-3-31 12:35
https://doi.org/10.1007/978-3-658-19455-0ion, .oss, .hange and .nnovation, and it is called .. This is the first such model rigorously analysed. The focus of the paper is around the size distribution of gene families. The formulas for equilibrium gene family sizes are derived showing that they follow a logarithmic distribution. We consider作者: Interregnum 時間: 2025-3-31 14:51 作者: GRIN 時間: 2025-3-31 19:39 作者: Agility 時間: 2025-3-31 22:23 作者: 連累 時間: 2025-4-1 03:10 作者: 抗體 時間: 2025-4-1 07:37 作者: VEIL 時間: 2025-4-1 12:39
Sociological Perspectives on Labor Markets the problem of ordering the contigs of two partially assembled genomes so as to maximize the similarity (measured in terms of genome rearrangements) between the assembled genomes. We give a linear-time algorithm for the .: Given two signed permutations (genomes) that are been broken into blocks (co
