Liquid-liquid phase separation sequence-based predictors
Here we will revise the state-of-the-art LLPS sequence-based predictors, briefly introducing them and explaining which are the ... LLPS often involves sequence regions that have unique functional characteristics, as well as the presence of prion-like and RNA ... Shea, Joan-Emma; Best, Robert B; Mittal, Jeetain (2021-04-01). "Physics-based computational and theoretical approaches to ... trying to understand the relationship between protein sequence properties and the capability to drive LLPS. ...
Gijswijt's sequence
The sequence is base-agnostic. That is, if a run of 10 repeated blocks is found, the next term in the sequence would be a ... Look-and-say sequence Kolakoski sequence Autogram Sloane, N. J. A. (ed.). "Sequence A090822 (Gijswijt's sequence: a(1) = 1; for ... The sequence can be broken into discrete "block" and "glue" sequences, which can be used to recursively build up the sequence. ... sequence A090822 in the OEIS) The sequence is similar in definition to the Kolakoski sequence, but instead of counting the ...
Shine-Dalgarno sequence
The six-base consensus sequence is AGGAGG; in Escherichia coli, for example, the sequence is AGGAGGU, while the shorter GAGG ... Base pairing between the 3'-end of the rRNA and the Shine-Dalgarno sequence in mRNA is a mechanism by which the cell can ... terminal 16S rRNA sequence can restore translation. Kozak consensus sequence, the sequence that targets the ribosome to the ... Many studies have confirmed that base pairing between the Shine-Dalgarno sequence in mRNA and the 3' end of 16S rRNA is of ...
ChIP sequencing
Templates are sequenced base-by-base during each read. Then, the data collection and analysis software aligns sample sequences ... Sequencing, by contrast, is thought to have less bias, although the sequencing bias of different sequencing technologies is not ... There are many new sequencing methods used in this sequencing step. Some technologies that analyze the sequences can use ... Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction ...
Nanopore sequencing
... each base could be converted to one sequence instead of two), will sequence over 500 bases per second. Advantages of this ... Instead of one base being identified as it translocates through the pore, ~12 bases are required to find the sequence of one ... This sequencing method has a capacity of 50-250 bases per second per pore, and a four color fluorophore system ( ... V.7, -N.5, -P.467-473 Liu Z, Wang Y, Deng T, Chen Q (2016-05-30). "Solid-State Nanopore-Based DNA Sequencing Technology". ...
Whole genome bisulfite sequencing
... perform comprehensive assays based on sequencing-by-synthesis of base pairs. Following library amplification, a series of ... Reduced representation bisulfite sequencing DNA methylation Shotgun sequencing ChIP-sequencing Kawakatsu, Taiji (2020), ... which affects sequences with highly skewed base compositions due to high rates of polymerase sequence errors in high AT-content ... One of the biggest concerns is the potential of bias in the base composition of sequences and over-representation of methylated ...
Sequence clustering
The similarity score is often based on sequence alignment. Sequence clustering is often used to make a non-redundant set of ... In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences ... sequences CluSTr: A single-linkage protein sequence clustering database from Smith-Waterman sequence similarities; covers over ... CD-HIT UCLUST in USEARCH Starcode: a fast sequence clustering algorithm based on exact all-pairs search. OrthoFinder: a fast, ...
Illumina dye sequencing
... is a technique used to determine the series of base pairs in DNA, also known as DNA sequencing. The ... "History of Illumina Sequencing". Archived from the original on 12 October 2014. "Illumina - Sequencing and array-based ... This technique offers several advantages over traditional sequencing methods such as Sanger sequencing. Sanger sequencing ... the barcode sequence (indices), and the binding site for the sequencing primer. Indices are usually six base pairs long and are ...
Massive parallel sequencing
... very different from that of Sanger sequencing-also known as capillary sequencing or first-generation sequencing-which is based ... Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing ... Clinical metagenomic sequencing First-generation sequencing Third-generation sequencing RNA Velocity Nyren, P.; Pettersson, B ... January 2010). "Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays". Science. 327 (5961): 78- ...
Aronson's sequence
Weisstein, Eric W. "Aronson's Sequence". MathWorld. (Articles with short description, Short description matches Wikidata, Base- ... Aronson's sequence is an integer sequence defined by the English sentence "T is the first, fourth, eleventh, sixteenth, ... ... Cloitre, Sloane & Vandermast (2003) write that Aronson's sequence is "a classic example of a self-referential sequence." ... the sequence is credited to Jeffrey Aronson of Oxford, England. The sequence is infinite-and this statement requires some proof ...
Bisulfite sequencing
Figure 2). Although most other modalities are not true sequencing-based techniques, the term "bisulfite sequencing" is often ... Bisulfite sequencing (also known as bisulphite sequencing) is the use of bisulfite treatment of DNA before routine sequencing ... This is based on a multi-tiered strategy, whereby bisulfite sequencing is used to obtain high-resolution methylation profiles ... Oxidative bisulfite sequencing is a method to discriminate between 5-methylcytosine and 5-hydroxymethylcytosine at single base ...
DNA sequencing
Shotgun sequencing is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to and ... RNA sequencing was one of the earliest forms of nucleotide sequencing. The major landmark of RNA sequencing is the sequence of ... Two main areas of nanopore sequencing in development are solid state nanopore sequencing, and protein based nanopore sequencing ... 0.75 per base. Meanwhile, sequencing of human cDNA sequences called expressed sequence tags began in Craig Venter's lab, an ...
Single-molecule real-time sequencing
... they extend sequencing read lengths to an average of approximately 8,500 bases, with the longest reads exceeding 30,000 bases. ... Throughput varies based on the type of sample being sequenced. With the introduction of P6-C4 chemistry typical throughput per ... sequencing is a parallelized single molecule DNA sequencing method. Single-molecule real-time sequencing utilizes a zero-mode ... This P4 enzyme has average read lengths of more than 4,300 bases when paired with the C2 sequencing chemistry and more than ...
Reduced representation bisulfite sequencing
Now, next generation sequencing approaches are used. For Illumina sequencing, 36-base single-end sequencing reads are most ... Sequencing: The fragments are then sequenced. When RRBS was first developed, Sanger sequencing was initially used. ... Finally, Anchor-Based Bisulfite Sequencing (ABBS) was developed by Ben Delatte's group at Active Motif. This technology uses ... According to Gu et al., DNA fragments of 40-220 base pair are representative of the majority of promoter sequences and CpG ...
Nucleic acid sequence
One sequence can be complementary to another sequence, meaning that they have the base on each position in the complementary (i ... DNA sequencing is the process of determining the nucleotide sequence of a given DNA fragment. The sequence of the DNA of a ... Digital genetic sequences may be stored in sequence databases, be analyzed (see Sequence analysis below), be digitally altered ... In bioinformatics, a sequence entropy, also known as sequence complexity or information profile, is a numerical sequence ...
Clinical metagenomic sequencing
Boolchandani, Manish; D'Souza, Alaric W.; Dantas, Gautam (June 2019). "Sequencing-based methods and resources to study ... High-throughput sequencing: all the nucleic acids fragments of the library are sequenced. The sequencing platform to be used is ... Sequencing Clinical data management Nanopore sequencing Govender, Kumeren N.; Street, Teresa L.; Sanderson, Nicholas D.; Eyre, ... The untargeted analysis is a metagenomic Shotgun sequencing approach. The whole DNA and/or RNA is sequenced with this approach ...
End-sequence profiling
... (ESP) (sometimes "Paired-end mapping (PEM)") is a method based on sequence-tagged connectors developed ... "End-sequence profiling: Sequence-based analysis of aberrant genomes". Proceedings of the National Academy of Sciences. 100 (13 ... From the BAC library, both ends of the inserted fragments are sequenced using a sequencing platform. Detection of variations is ... Approximately 100-200 tumors can be sequenced at a resolution greater than 150kb when compared to sequencing an entire genome. ...
Oligotyping (sequencing)
DNA sequences were originally read from sequencing gels by eye. With the advent of computerized base callers, humans no longer ... Oligotyping is the process of correcting DNA sequence measured during the process of DNA sequencing based on frequency data of ... With the advent of high throughput sequencing, the volume of sequence to be corrected exceeded human capacity for sequence ... called' the bases and instead 'corrected' the called bases. The bases were called by the software using the relative intensity ...
Conserved sequence
However, sequence conservation in ncRNAs is generally poor compared to protein-coding sequences, and base pairs that contribute ... Conserved sequences are typically identified by bioinformatics approaches based on sequence alignment. Advances in high- ... Sequences may also recombine or be deleted due to chromosomal rearrangements. Conserved sequences are sequences which persist ... orthologous sequences), or within a genome (paralogous sequences), or between donor and receptor taxa (xenologous sequences). ...
MicroRNA sequencing
... the raw sequence reads are filtered based on quality. The adaptor sequences are also trimmed off the raw sequence reads. The ... miRNA sequencing in and of itself is not a new idea, initial methods of sequencing utilized Sanger sequencing methods. ... polymerase-based sequence-by-synthesis on the Illumina (company) platform, or sequencing by ligation on the ABI Solid ... is the use of next-generation sequencing or massively parallel high-throughput DNA sequencing to sequence microRNAs, also ...
Burrows-Wheeler transform
... of which the first few bases are sequenced, yielding several millions of "reads", each 30 to 500 base pairs ("DNA characters") ... Ktistakis R, Fournier-Viger P, Puglisi SJ, Raman R (2019). "Succinct BWT-Based Sequence Prediction". Database and Expert ... nearly complete sequence of the organism in question (which may be up to several billion base pairs long). A number of ... The BWT can be defined with regards to the suffix array SA of text T as (1-based indexing): B W T [ i ] = { T [ S A [ i ] − 1 ...
NASBA (molecular biology)
Nucleic acid sequence-based amplification, commonly referred to as NASBA, is a method in molecular biology which is used to ... Mugasa, CM; Laurent, T; Schoone, GJ; Kager, PA; Lubega, GW; Schallig, HD (2009). "Nucleic acid sequence-based amplification ... Malek, L.; Sooknanan, R.; Compton, J. (1994). Nucleic acid sequence-based amplification (NASBA). Methods in Molecular Biology. ... Malek, L.; Sooknanan, R.; Compton, J. (1994). Nucleic acid sequence-based amplification (NASBA). Methods in Molecular Biology. ...
De novo sequence assemblers
The assembler will then construct sequences based on the De Bruijn graph. De Bruijn graph assemblers typically perform better ... De novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of ... Peltola, Hannu; Söderlund, Hans; Ukkonen, Esko (1984-01-11). "SEQAID: a DNA sequence assembling program based on a mathematical ... Sequence assembly Sequence alignment De novo transcriptome assembly J. Bang-Jensen; G. Gutin; A. Yeo (2004). "When the greedy ...
De novo peptide sequencing
Based on the sequence list, it generates complete sequences in spectra and scores them with the experimental spectrum. However ... Given previously predicted partial peptide sequence, neural-network-based de novo peptide sequencing models will repeatedly ... based de novo peptide sequencing algorithms can also be fast enough to achieve real-time peptide de novo sequencing. PEAKS ... proposed DeepNovo, the first deep learning based de novo sequencing software. The benchmark analysis in the original ...
Sequence-controlled polymer
DNA, based on A-T, C-G base pairs, are formed in well-aligned sequences. Through precise sequences of DNA, 20 amino acids are ... A sequence-controlled polymer is a macromolecule, in which the sequence of monomers is controlled to some degree. This control ... The property of sequence control make sequence-controlled polymers an ideal platform to install various kinds of pendants (like ... 2. Principle of sequence regulation and synthesis of sequence-regulated oligomers of functional vinyl ethers and styrene ...
Simple sequence length polymorphism
... a difference in DNA sequence amongst individuals. SSLPs are repeated sequences over varying base lengths in intergenic regions ... Simple Sequence Length Polymorphisms (SSLPs) are used as genetic markers with polymerase chain reaction (PCR). An SSLP is a ...
Fusarium oxysporum f.sp. cubense
"Fungal taxonomy and sequence-based nomenclature". Nature Microbiology. Nature Portfolio. 6 (5): 540-548. doi:10.1038/s41564-021 ... Other post-sequencing data analysis performed by the disequilibrium study also failed to reject recombination however this ... Memon, Komal; Umrani, Fahim Aziz; Baqai, Attiya; Syed, Zafi Sherhan (2023). A Review Based On Comparative Analysis of ...
777 (number)
Sloane, N. J. A. (ed.). "Sequence A002113 (Palindromes in base 10)". The On-Line Encyclopedia of Integer Sequences. OEIS ... Sloane, N. J. A. (ed.). "Sequence A046760 (Wasteful numbers)". The On-Line Encyclopedia of Integer Sequences. OEIS Foundation. ... Sloane, N. J. A. (ed.). "Sequence A000959 (Lucky numbers)". The On-Line Encyclopedia of Integer Sequences. OEIS Foundation. ... Sloane, N. J. A. (ed.). "Sequence A005100 (Deficient numbers)". The On-Line Encyclopedia of Integer Sequences. OEIS Foundation ...
List of Fusarium species
"Fungal taxonomy and sequence-based nomenclature". Nature Microbiology. Nature Portfolio. 6 (5): 540-548. doi:10.1038/s41564-021 ... This list is based on the EOL list and was updated with the Species Fungorum list in 2023. Fusarium aberrans J.W. Xia, L. ...
11 (number)
Sloane, N. J. A. (ed.). "Sequence A002113 (Palindromes in base 10.)". The On-Line Encyclopedia of Integer Sequences. OEIS ... Sloane, N. J. A. (ed.). "Sequence A001359 (Lesser of twin primes.)". The On-Line Encyclopedia of Integer Sequences. OEIS ... The On-Line Encyclopedia of Integer Sequences. OEIS Foundation. Retrieved 2018-11-20. Sloane, N. J. A. (ed.). "Sequence A051634 ... In duodecimal and higher bases (such as hexadecimal), 11 is represented as B, E, Z or ↋ (el), where 10 is A, T, W, X or ↊ (dek ...