Alignment-free approaches have been used in sequence similarity searches, clustering and classification of sequences, and more recently in phylogenetics (Figure 1). (wikipedia.org)
Random similarity of sequences or sequence sections can impede phylogenetic analyses or the identification of gene homologies. (leibniz-lib.de)
It is therefore important to identify possible random similarity within sequence alignments in advance of model estimation and tree reconstructions. (leibniz-lib.de)
We propose an alternative method which can identify random similarity within multiple sequence alignments based on Monte Carlo resampling within a sliding window. (leibniz-lib.de)
The method infers similarity profiles from pairwise sequence comparisons and subsequently calculates a consensus profile. (leibniz-lib.de)
In consequence, consensus profiles identify dominating patterns of non-random similarity or randomness within sections of multiple sequence alignments. (leibniz-lib.de)
many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA (tRNA) or microRNA (miRNA), is observed. (wikipedia.org)
Bioinformatics3
In bioinformatics, alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives over alignment-based approaches. (wikipedia.org)
Molecular sequence and structure data of DNA, RNA, and proteins, gene expression profiles or microarray data, metabolic pathway data are some of the major types of data being analysed in bioinformatics. (wikipedia.org)
Since the origin of bioinformatics, sequence analysis has remained the major area of research with wide range of applications in database searching, genome annotation, comparative genomics, molecular phylogeny and gene prediction. (wikipedia.org)
Divergence2
The pair wise distance between two sequences is then calculated Jensen-Shannon (JS) divergence between their respective FFPs. (wikipedia.org)
Sequence divergence within oligonucleotide-binding sites creates primer-template duplex instability and lowers T m . (nature.com)
Comparative5
The size of this sequence data poses challenges on alignment-based algorithms in their assembly, annotation and comparative studies. (wikipedia.org)
To provide a fresh and less-biased global set of analyses, large-scale comparative DNA sequence alignments between the chimpanzee and human genomes were performed with the BLASTN algorithm. (icr.org)
Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. (plos.org)
When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. (plos.org)
Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known). (wikipedia.org)
Analyses1
Such molecular phylogeny analyses employing alignment-free approaches are said to be part of next-generation phylogenomics. (wikipedia.org)
Algorithms1
This program switches between different alignment algorithms and between sequences and profiles, so I wanted to create a library that aligns any collection of objects with various algorithms using the same syntax. (github.com)
Cosine distance function is then used to compute pairwise distance between CVs of sequences. (wikipedia.org)
Protein3
The methodology involved in FFP based method starts by calculating the count of each possible k-mer (possible number of k-mers for nucleotide sequence: 4k, while that for protein sequence: 20k) in sequences. (wikipedia.org)
It started in 1999 from C code that I had created for a program called RADAR that is used to find repeats in protein sequences. (github.com)
One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
Multiple3
A multiple alignments is then a collection of Alignatum objects. (github.com)
This is facilitated by directing primer and probe design to evolutionarily conserved regions identified through multiple sequence alignments that portray geographical and temporal genomic variability. (nature.com)
The approach has been extended to aminoacid and nucleotide data and is currently further developed to visualize total randomness among sequences of a multiple sequence alignment together with Dr. Patrick Kück and Sandra Meid, both ZFMK. (leibniz-lib.de)
Nucleotide2
The use of low complexity sequence masking had the effect of decreasing computational time about 5-6 fold, lengthening the alignments slightly, lowering the number of database hits, and lowering the percent nucleotide identity slightly. (icr.org)
qPCR probe design is more averse to similar modifications because increasing probe T m through nucleotide degeneracy or sequence lengthening may lead to high T m variations that reduce specific target discrimination. (nature.com)
Subsequently1
The chimp sequences were subsequently implicated by personal correspondence with NCBI staff and supporting data from this study to be pre-screened for some level of homology to the human genome. (icr.org)
Computational2
Another limitation of alignment-based approaches is their computational complexity and are time-consuming and thus, are limited when dealing with large-scale sequence data. (wikipedia.org)
Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. (wikipedia.org)
Perform1
Other classes ending in -or perform other tasks like building trees (Treetor) or weight sequences (Weightor) Alignata: things that have been aligned. (github.com)
Approaches3
Alignment-based approaches generally give excellent results when the sequences under study are closely related and can be reliably aligned, but when the sequences are divergent, a reliable alignment cannot be obtained and hence the applications of sequence alignment are limited. (wikipedia.org)
Different approaches have been already suggested to identify and treat problematic alignment sections, like GBLOCKS or noisy. (leibniz-lib.de)
The result is that its SNP predictions are more accurate than other SNP prediction approaches used today that start from the most probable sequence, including those using base quality. (seqanswers.com)
Frequency3
Alignment-free methods can broadly be classified into five categories: a) methods based on k-mer/word frequency, b) methods based on the length of common substrings, c) methods based on the number of (spaced) word matches, d) methods based on micro-alignments, e) methods based on information theory and f) methods based on graphical representation. (wikipedia.org)
This leads to conversion of each sequence into its feature frequency profile. (wikipedia.org)
In this method frequency of appearance of each possible k-mer in a given sequence is calculated. (wikipedia.org)
Calculate1
The RTD based method does not calculate the count of k-mers in sequences, instead it computes the time required for the reappearance of k-mers. (wikipedia.org)
Add sequences to the project and align some or all of them . (dnastar.com)
If all sequences were aligned, add more sequences to the project. (dnastar.com)
The menu command and tool are enabled only if the project contains an alignment and at least one unaligned sequence. (dnastar.com)
The 1000 genomes project recalibrated their FASTQ files using prior alignment information to improve the data quality. (seqanswers.com)
Total1
Each k-mer count in each sequence is then normalized by dividing it by total of all k-mers' count in that sequence. (wikipedia.org)
Data1
The advent of next-generation sequencing technologies has resulted in generation of voluminous sequencing data. (wikipedia.org)
Results2
Despite the reliance of clinical virology on qPCR, technical challenges persist that compromise their reliability for sustainable epidemic containment as sequence instability in probe-binding regions produces false-negative results. (nature.com)
RESULTS: Compared with other aligners, Slider has higher alignment accuracy and efficiency. (seqanswers.com)
One group of experiments was conducted with query and subject low-complexity sequence masking enabled while the second set had masking parameters disabled. (icr.org)
Additionally, randomly similar sequences or ambiguously aligned sequence sections can negatively interfere with the estimation of substitution model parameters. (leibniz-lib.de)
Profiles1
This somewhat explains my naming convention: Alignandum: something that is to be aligned, to-date these are sequences and profiles. (github.com)
Length1
The average chimp query sequence length was 740 bases and depending on the BLASTN parameter combination, average alignment length varied between 121 and 191 bases. (icr.org)
Determine1
A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule given only a nucleic acid sequence. (wikipedia.org)
Distance2
For each secondary structure element (helices and strands), the average normalized covariation score was based on the sequence distance relative to an initial position. (biomedcentral.com)
Curves connecting the average covariation scores at each sequence distance are drawn as cubic splines. (biomedcentral.com)
Identity1
The etiological agent, SARS-CoV-2, is a member of the Coronaviridae family including SARS-CoV-1 (2002-2004) and MERS-CoV (since 2012), with the sequence identity of 79.6% and 50%, respectively. (biorxiv.org)
Step1
optional) An upcoming step will overwrite the current alignment. (dnastar.com)
Structure1
Secondary structure can be predicted from one or several nucleic acid sequences. (wikipedia.org)