Alignment-free
Fast-SG: an alignment-free algorithm for hybrid assembly
... Abstract Background: Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are ...
16
Application of Lempel-Ziv complexity to alignment-free sequence comparison of protein families
... of alignment-free methods have been pro- posed to overcome the limitations of the alignment-based se- quence comparisons (reviewed by Vinga and Almeida, ...
1
Self-eclipsing: alignment-free vortex coronagraphy
... illustrated in Fig. 5(a) where the dynamics of the self induced vortex mask observed between crossed circular polarizers is shown at different times t, the laser being switched on at t 0, for on axis illumination with ...
5
Rapid alignment-free phylogenetic identification of metagenomic sequences
... (Rapid Alignment-free Phylogenetic Placement via Ancestral ...reference alignment, (ii) QSs are then placed on the tree by matching their k-mers against the database of ...scalable, ...
11
Rapid alignment-free phylogenetic identification of metagenomic sequences
... (Rapid Alignment-free Phylogenetic Placement via Ancestral ...reference alignment, (ii) QSs are then placed on the tree by matching their k-mers against the database of ...scalable, ...
11
RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes
... New methods have emerged for both the storage and analysis of pan-genomes. These methods usually use the same approach, which consists of storing a reference sequence and information on each genome variation compared to ...
29
Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis
... that alignment heuris- tics often create systematic biases that affect analysis [ 26 , 42 ...rough alignment suffices for an accurate tree reconstruction (bypassing the computationally difficult multiple ...
31
Application of the Lempel-Ziv complexity to the alignment-free sequence comparison of protein families
... outperforms all other methods at the three lower levels of the SCOP classification, except the very slow SW local alignment at the family level. at superfamily and fold levels, our seq[r] ...
27
Alignment-Free Phylogenetic Reconstruction
... In this section, we show how to define an appropriate notion of “evolutionary distance” between two species. Although such distances have been widely used in prior phylogenetic work and have been defined for a variety of ...
23
DALIX: optimal DALI protein structure alignment
... Abstract: We present a mathematical model and exact algorithm for protein structure align- ment using DALI scoring, which is an NP-hard problem. DALI scoring is based on comparing the inter-residue distance matrices of ...
22
Towards a complex alignment evaluation dataset
... to the repository administrator: tech-oatao@listes-diff.inp-toulouse.fr This is an author’s version published in: https://oatao.univ-toulouse.fr/22205 To cite this version: Thiéblin, Elodie and Haemmerlé, Ollivier and ...
3
Gesture / speech alignment in weather reports
... gesture-speech alignment rules observed by Loehr (2004), there is a mismatch of more than 200 ms in semantic content between what is referred to in speech and what is pointed at in the background screen for two ...
6
On subset seeds for protein alignment
... performance of B LASTP with word size 3 and the vector seed family from [4], for different score thresholds. The other curves show the performances of different seed alphabets from Sections III-IV represented by the ...
26
iPBA: a tool for protein structure comparison using sequence alignment strategies.: Structural Alphabet Alignment
... PB alignment then guides the 3D fitting of the structures by ProFit (36) ...the alignment is also provided along with the Aln_Score and ...incomplete alignment outputs provided by the ...
7
Explaining Argumentation over Alignment Agreements
... The user can run the system on command line by passing all the required input parameters: (a) name of each matcher used for finding the alignments; (b) RDF files which contain the alignments that matchers have generated; ...
8
4PL and models of strategic alignment
... NETCOM, vol. 21, n ° 3-4, 2007 401 to the particular case of 4PL development. Other research followed but did not try very hard to assess them empirically and to make them operational except for Bergeron et al. (2004). ...
15
Loop Alignment for Memory Accesses Optimization
... L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignemen[r] ...
16
Referential hierarchies and alignment: An overview
... 70s, alignment typology was based on the roles of the event participants that are represented by verbal ...characterization, alignment refers to the way the basic notions S (the single argument of ...
10
SOFYA: Semantic on-the-fly Relation Alignment
... Contributions. In this paper, we propose an instance-based on-the-fly approach for relation alignment between two KBs. Our method requires only a SPARQL endpoint for each dataset. Given a relation name in a source ...
3
Online Relation Alignment for Linked Datasets
... over the network for the different sample sizes in S r S . Note here, that a traditional schema-matching approach operating on a dataset snapshot, and as such they introduce an incomparably higher overhead in terms of ...
16