alignment-free
Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values
... impossible) to observe reads that are error-free. With such an increase in error rates, the ability to work with noisy reads is fundamental. Recently we proposed a set of alignment-free statistics, ...
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Alignment-free phylogeny of whole genomes using underlying subwords
... An important aspect in phylogeny reconstruction is the fact that gene-based methods strictly focus on compar- ing the coding regions of genomes, which can account for as little as 1% of the genomic sequence in humans ...
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Alignment-free classification of COI DNA barcode data with the Python package Alfie
... subsequent alignment of sequences for a group of interest can narrow the scope of the application of alignment methods and thereby im- prove both analysis speed and ...The alignment-free model ...
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AluMine: alignment-free method for the discovery of polymorphic Alu element insertions
... fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human ...an alignment-free genotyping method that uses the frequency of ...
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LAF: Logic Alignment Free and its application to bacterial genomes classification
... These numerical representations of the sequences allow the use of statistical and mathematical techniques; indeed, the most used approach for sequence comparisons in alignment-free vector representations ...
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MissMax: alignment-free sequence comparison with mismatches through filtering and heuristics
... of alignment free distances based on approximate matching, that are a promising approach to improve the quality of alignment free sequence com- ...
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Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
... Background: High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high ...
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Skmer: assembly free and alignment free sample identification using genome skims
... true alignment of the two genomes, we can compute the true genomic distance as the proportion of mismatches among aligned orthologous positions ...true alignment is ...an alignment-free ...
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Clustering of reads with alignment-free measures and quality values
... of alignment-free measures also allows the reconstruction of phylogenies for whole genomes ...Several alignment-free methods have been devised for the detection of enhancers in ChIP-Seq data ...
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Alignment free sequence comparison: benefits, applications, and tools
... Metagenomics, the study of genomic sequences ob- tained directly from the environment (e.g., aquatic ecosys- tems, human body), has become a primary application of alignment-free methods, in particular ...
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Molecular Distance Maps: An alignment-free computational tool for analyzing and visualizing DNA sequences' interrelationships
... Logic Alignment Free (LAF) was also introduced and applied to bacterial genomes in ...combines alignment-free techniques and rule-based classification to assign biological samples to their ...
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Use of the R-group descriptor for alignment-free QSAR
... The results obtained using the RGDs have been compared with those obtained using two existing methods for alignment-free QSAR: EVA (for EigenValue Analysis) [2] and HQSAR (for Hologram QSAR) [4]. EVA ...
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An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data
... The principal axes of a protein structure are computed directly from its atomic coordinates. The first moment of these points is their center of mass, and the three eigenvectors and eigenvalues of the second moment ten- ...
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Benchmarking of alignment free sequence comparison methods
... The reference data sets of protein family members shar- ing a high (≥ 40%) and low (< 40%) sequence identity were constructed based on two sections of the SCOPe database v. 2.07 [68], namely, ASTRAL95 and AS- TRAL40 ...
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Evaluating the Significance of Global and Local Features in Expressed Sequence Tag: A Clustering Quality Perspective
... Another clustering algorithm that is alignment free is Xsact [13]. It uses a suffix array, a lexicographically ordered array of all suffixes of the EST sequences. Radix sort is used to generate the suffix ...
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Secured Fingerprint based Crypto System with Reversible Watermarking Scheme
... Double layer structure check (DLSC) unique mark confirmation plot intended for biometric portable layout insurance, school of software engineering and itrmit college melbourne, kai xi and jiankun hu Australia,2013[6].In ...
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Performance Evaluation of Biometric Cryptosystem Using Fuzzy Vault
... Cai Li, Jiankun Hu, “A Security-enhanced Alignment-free Fuzzy Vault-based Fingerprint Cryptosystem Using Pair-polar Minutiae Structures”, IEEE Transactions on Information Forensics and S[r] ...
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KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation
... Results: To meet increasing demands for comparing large genome sequences and to promote the use of the K- mer approach, we develop a versatile database, KGCAK (http://kgcak.big.ac.cn/KGCAK/), containing ~8,000 genomes ...
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Therapeutic journey of synthetic betacarboline derivatives: A short review
... An alignment-free, three dimensional quantitative structure-activity relationship (3D- QSAR) analysis has been performed on a series of - carboline derivatives as potent antit[r] ...
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Mapping the progression of non carious cervical lesions
... Data alignment, Mapping and alignment precision (DSMatch - Sequential alignment, Varying grid interval and exclusion threshold, Varying exclusion threshold; Polyworks - Sequential alignment, ...
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