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Method of DNA sequence reconstruction
bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is
Sequence_assembly
Computational analysis of large, complex sets of biological data
visualization. Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment
Bioinformatics
Substrings of length k contained in a biological sequence
k} contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which k-mers are composed
K-mer
Topics referred to by the same term
without external direction Sequence assembly, a process to reconstruct a long DNA sequence from numerous fragments Assembly rules, set of controversial
Assembly
Measurement in DNA sequencing
used DNA sequence assembly programs in the biotech industry. Phrap uses Phred quality scores to determine highly accurate consensus sequences and to estimate
Phred_quality_score
Identification and study of genomic sequences
In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand
Sequence_analysis
Software in bioinformatics
reach a global optimum in the assembly, and do not perform well on read sets that contain repeat regions. Early de novo sequence assemblers, such as SEQAID
De_novo_sequence_assemblers
Method used for sequencing random DNA strands
original sequence is reconstructed from the reads using sequence assembly software. First, overlapping reads are collected into longer composite sequences known
Shotgun_sequencing
De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome. As a result
De novo transcriptome assembly
De_novo_transcriptome_assembly
transcripts using sequence assembly. Two main categories of sequence assembly are often distinguished: de novo transcriptome assembly - especially important
Phylogenetic inference using transcriptomic data
Phylogenetic_inference_using_transcriptomic_data
Discipline in genetics
higher. Sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is
Genomics
Process of determining the nucleic acid sequence
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is
DNA_sequencing
Digital nucleic acid sequence database
genome assembly that represents the complete genetic sequence of an organism as a continuous string of nucleotides (A, T, C, and G). For an assembly to serve
Reference_genome
hybrid genome assembly refers to utilizing various sequencing technologies to achieve the task of assembling a genome from fragmented, sequenced DNA resulting
Hybrid_genome_assembly
Patterns of nucleic acids that occur in multiple copies throughout the genome
Repeated sequences (also known as repetitive elements, repeating units or repeats) are short or long patterns that occur in multiple copies throughout
Repeated_sequence_(DNA)
DNA sequence assembly software
Staden Package is computer software, a set of tools for DNA sequence assembly, editing, and sequence analysis. It is open-source software, released under a
Staden_Package
Molecular cloning method for DNA assembly
re-forming the original sequence, this will be susceptible to further cutting throughout the assembly reaction. Restriction enzyme DNA assembly has cloning standards
Golden_Gate_Cloning
Type of database index
sequence assembly of short fragments of sequenced DNA. One way to find the source of a fragment is to search for it against a reference DNA sequence.
Inverted_index
Topics referred to by the same term
reference genome, using de novo sequence assembly De novo gene birth, the emergence of genes from non-coding sequence De novo domestication, the domestication
De_novo
finishing DNA sequence assemblies. Originally developed for sequence assemblies created with phrap, recent versions also support other sequence assembly programs
Consed
individuals. They are used in shotgun sequencing, specifically to aid sequence assembly. STSs are very helpful for detecting microdeletions in some genes
Sequence-tagged_site
French software company
environment dedicated to microbial research.[citation needed] This covers sequence assembly, mapping, annotation transfer and identification of protein domains
Genostar
2000 studio album by Queens of the Stone Age
Bradley Cook – additional recording (tracks 8, 9) Martin Schmelzle – sequence & assembly engineer Dan Druff – guitar technician Robert Brunner – pre-production
Rated R (Queens of the Stone Age album)
Rated_R_(Queens_of_the_Stone_Age_album)
Algorithm package
genome assembly and short read sequencing alignments. This is achieved through the manipulation of de Bruijn graphs for genomic sequence assembly via the
Velvet_assembler
Online database from the EBI on Nucleotides
annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata
European_Nucleotide_Archive
minor differences between the sequences of interest. Spaced seeds have been used in homology search., alignment, assembly, and metagenomics. They are usually
Spaced_seed
Cereal grass and grain
hampered by the lack of a reference genome assembly. In May 2022, a fully annotated reference genome sequence of Avena sativa was reported. The AA subgenome
Oat
Velvet: a set of algorithms manipulating de Bruijn graphs for genomic sequence assembly Geohash: a public domain algorithm that encodes a decimal latitude/longitude
List_of_algorithms
DNA sequencing method
areas. Also, if the sequence is de novo and a reference does not exist, repeated areas can cause a lot of difficulty in sequence assembly. Additional difficulties
Illumina_dye_sequencing
Set of overlapping DNA segments that together represent a consensus region of DNA
genome that is used to guide sequencing and assembly. Contigs can thus refer both to overlapping DNA sequences and to overlapping physical segments (fragments)
Contig
Method of DNA sequencing developed in 1977
templates needed to sequence DNA contigs at a given redundancy. Microfluidics may allow for faster, cheaper and easier sequence assembly. Maxam–Gilbert sequencing
Sanger_sequencing
Group of methods in synthetic biology
candidate clones confirming the sequence of the cloned synthetic gene by automated sequencing methods. Moreover, because the assembly of the full-length gene
Artificial_gene_synthesis
Selective medium Self Self-assembly Self-fertilization Selfed Selfish DNA Sense strand Sequence Sequence assembly Sequence tagged site Sequencing Sex
Index_of_genetics_articles
Topics referred to by the same term
(Texas), two ranches SPAdes (software), a set of tools for genomic sequence assembly SMART Process Acceleration Development Environment Spade (political
Spade_(disambiguation)
American super heavy-lift expendable rocket
electrical control subsystem are the power and control distributors, the sequencer assemblies, and the pressure sensing and control devices. The S-IVB instrumentation
Saturn_V
Process in computational biology
of a gene based on its sequence alone. Gene prediction is one of the key steps in genome annotation, following sequence assembly, the filtering of non-coding
Gene_prediction
Standard for components used in DNA synthesis
BioBrick parts are DNA sequences which conform to a restriction-enzyme assembly standard. These building blocks are used to design and assemble larger
BioBrick
Complete set of nucleic acid sequences for humans
The human genome is a complete set of DNA sequences for each of the 22 autosomes and the two distinct sex chromosomes (X and Y) in humans. A small DNA
Human_genome
Theory about the release of genetic sequence data
Automatic release of sequence assemblies larger than 1 kb (preferably within 24 hours). Immediate publication of finished annotated sequences. Aim to make the
Bermuda_Principles
American mathematician
A 1995 paper by Idury and Waterman introduced Eulerian-De Bruijn sequence assembly which is widely used in next-generation sequencing projects. With
Michael_Waterman
Low-level programming language family
assembly. Judicious commenting is essential in assembly language programs, as the meaning and purpose of a sequence of binary machine instructions can be difficult
Assembly_language
this approach for de novo assembly. Next-generation sequencing (NGS) methods have allowed the generation of new genome sequences much faster and cheaper
Bloom filters in bioinformatics
Bloom_filters_in_bioinformatics
Laboratory technique to multiply a DNA sample for study
knowledge of the target sequence. Assembly PCR or Polymerase Cycling Assembly (PCA): artificial synthesis of long DNA sequences by performing PCR on a
Polymerase_chain_reaction
Cereal grain
Sequencing Consortium (2012). "A physical, genetic and functional sequence assembly of the barley genome". Nature. 491 (7426): 711–716. Bibcode:2012Natur
Barley
International scientific research project (1990–2003)
genome assembly. Both the Celera and public approaches spent roughly $250 million on the production sequencing effort. For sequence assembly, Celera
Human_Genome_Project
Inventory strategy
Just in sequence (JIS) is an inventory strategy that matches just in time (JIT) and complete fit in sequence with variation of assembly line production
Just_in_sequence
for DNA sequence assembly. It is part of the Phred-Phrap-Consed package. Phrap was originally developed by Prof. Phil Green for the assembly of cosmids
Phrap
Bioinformatics software work suite
design and analysis, global and local sequence alignment, similarity search, laboratory scale sequence assembly projects A comprehensive set of tools
Clone_manager
Software for DNA sequencing
Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing
Newbler
alphabetical order. A typical entry reports information in the following sequence: Name, age, country of citizenship at birth, subsequent nationality (if
Deaths_in_2026
features of DNA sequences CAF – Common Assembly Format for sequence assembly CRAM – compressed file format for storing biological sequences aligned to a
List_of_file_formats
Computer software for bioinformatics
biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. UGENE integrates dozens
UGENE
program for viewing, editing, and finishing DNA sequence assemblies. ACE files are generated by various assembly programs, including Phrap, CAP3, Newbler, Arachne
ACE_(genomic_file_format)
Common term for several varieties of coconut
Mueller, Lukas A; Galvez, Hayde F (1 August 2019). "De Novo Genome Sequence Assembly of Dwarf Coconut ( Cocos nucifera L. 'Catigan Green Dwarf') Provides
Dwarf_coconut
Hultin E, Dillner J (August 2020). "De novo sequence assembly requires bioinformatic checking of chimeric sequences". PLOS ONE. 15 (8) e0237455. Bibcode:2020PLoSO
Viral_metagenomics
Species of single-celled organism
Sillito, Dean; Clarke, Wayne E.; Uzuhashi, Shihomi (2011). "De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic
Albugo_candida
Manufacturing process
According to Henry Ford: The principles of assembly are these: (1) Place the tools and the men in the sequence of the operation so that each component part
Assembly_line
Former research initiative
systems for assembly of massive sequence data sets. No single assembly algorithm addresses all the known problems of assembling short-length sequences, so next-generation
Human_Microbiome_Project
Method of genome sequencing
addition to the assembly of the smaller organellar genomes, genome skimming can also be used to uncover conserved ortholog sequences for phylogenomic
Genome_skimming
Process in bioinformatics that identifies equivalent sites within molecular sequences
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence
Sequence_alignment
Single-molecule sequencing technology
the assembly. In addition, long Sanger reads are able to span most regions of repetitive DNA sequence which otherwise confound sequence assembly by causing
Transmission electron microscopy DNA sequencing
Transmission_electron_microscopy_DNA_sequencing
Individual differences in genomic DNA
novo sequence assembly may be applied with reads that are accurate enough. While, in practice, use of this method is limited by the length of sequence reads
Structural_variation
software for molecular mechanics modeling Earth BioGenome Project List of sequence alignment software List of open-source healthcare software List of biomedical
List of open-source bioinformatics software
List_of_open-source_bioinformatics_software
All genetic material of an organism
been sequenced and various regions have been annotated. The first genome to be sequenced was that of the virus φX174 in 1977; the first genome sequence of
Genome
Topics referred to by the same term
instruction in the ARM Cortex-M processor de Bruijn Graph, an approach to sequence assembly in computational biology Debug module, a type of background debug
DBG
Description of the structure and function of a genome
sections. The quality of the sequence assembly influences the quality of the annotation, so it is important to assess assembly quality before performing
DNA_annotation
Indian-American computer scientist
pattern matching, data structure simulations, universal graphs, DNA sequence assembly, derandomization and investigations of immune system responses. In
S._Rao_Kosaraju
DNA sequence software
CodonCode Aligner is a commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows. Features include chromatogram
CodonCode_Aligner
Nucleic acid motif in molecular biology
The Kozak consensus sequence (Kozak consensus or Kozak sequence) is a nucleic acid sequence that functions as the protein translation initiation site
Kozak_consensus_sequence
Transcript Assemblies database in computational biology is a repository of sequences collected for the construction of transcript assemblies. TIGR plant
TIGR plant transcript assembly database
TIGR_plant_transcript_assembly_database
This list of sequenced animal genomes contains animal species for which complete genome sequences have been assembled, annotated and published. Substantially
List of sequenced animal genomes
List_of_sequenced_animal_genomes
French biologist
Consortium; et al. (November 2012). "A physical, genetic and functional sequence assembly of the barley genome". Nature. 491 (7426): 711–716. Bibcode:2012Natur
Hélène_Bergès
used DNA sequence assembly programs in the biotech industry. Phrap uses Phred quality scores to determine highly accurate consensus sequences and to estimate
Phred_(software)
extensively to accelerate sequence production. He wrote the sequence CAFtools assembly pipeline which was used for the pipeline assembly of the human and other
Richard_Mott_(statistician)
Branch of phylogeny that analyzes genetic, hereditary molecular differences
a phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test (testing best-fitting substitution
Molecular_phylogenetics
Biochemical method in mass spectrometry
method in which a peptide amino acid sequence is determined from tandem mass spectrometry. Knowing the amino acid sequence of peptides from a protein digest
De_novo_peptide_sequencing
Species of legume
of the funding. By 2009, 84% of the genome assembly had been completed. The assembly of the genome sequence in M. truncatula was based on bacterial artificial
Medicago_truncatula
Genus of bacteria
Project (HMP), the genome of Abiotrophia defectiva ATCC 49176 has been sequenced (assembly) as it is a resident of human oral cavity and urogenital and intestinal
Abiotrophia
Gibson Assembly is a single-step, isothermal reaction with larger sequence-length capacity; ergo, it is used in place of Polymerase Cycling Assembly for
Synthetic_genomes
(currently vacant) and the Prime Minister of Azerbaijan, in that sequence. National Assembly of Azerbaijan Parliament of the Azerbaijan Democratic Republic
Speaker of the National Assembly of Azerbaijan
Speaker_of_the_National_Assembly_of_Azerbaijan
Polymerase cycling assembly (or PCA, also known as Assembly PCR) is a method for the assembly of large DNA oligonucleotides from shorter fragments. The
Polymerase_cycling_assembly
Genus of lichen-forming fungi
Chandler; Booth, Brendan; Allen, Jessica L. (2023). "Chromosomal genome sequence assembly and mating-type (MAT) locus characterization of the leprose asexual
Lepraria
Analysis of large datasets to understand living systems
advanced algorithms to perform data processing steps such as sequence assembly and sequence alignment for quality control. Some of these algorithms, such
Biomedical_data_science
Topics referred to by the same term
the United States Velvet assembler, a set of algorithms for genomic sequence assembly Velvet Divorce, the dissolution of Czechoslovakia in 1993 Velvet Revolution
Velvet_(disambiguation)
Automobile factory in Roanoke, Indiana, U.S.
shops, a paint shop, general assembly, and a sequence center. It assumed operations of the former Pontiac Truck and Bus Assembly. The factory is located at
Fort_Wayne_Assembly
Pakistani American plant geneticist
Dr. Khan co-led a research and completed a chromosome-scale genome sequence assembly of Honeycrisp apples. Tegtmeier R, Pompili V, Singh J, Micheletti
Awais_Khan_(plant_geneticist)
This list of sequenced plant genomes contains plant species known to have publicly available complete genome sequences that have been assembled, annotated
List of sequenced plant genomes
List_of_sequenced_plant_genomes
Legislative Assembly constituency in Manipur State, India
the Indian state of Manipur. In terms of sequence of Manipur state assembly constituencies, Khundrakpam Assembly constituency is numbered first among the
Khundrakpam Assembly constituency
Khundrakpam_Assembly_constituency
Echinoderm genomic database
protein sequences and interactants. Genomic research tools are implemented to assist browsing, search and analysis and visualization of genomic sequence assemblies
Echinobase
and aggressively clean sequence reads (gDNA or cDNA) prior to assembly. It takes in and returns fastq or fasta formatted sequence files. ShortRead is a
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
Bioinformatics company in Michigan, US
Washtenaw County Fast Track Award. Sequencher receives the Best DNA Sequence Assembly Product from the Biotechnology Software & Internet Journal. Gene Codes
Gene_Codes_Corporation
Mathematical sequence
the Prüfer sequence (also Prüfer code or Prüfer numbers) of a labeled tree is a unique sequence associated with the tree. The sequence for a tree on
Prüfer_sequence
Jeffrey D (July 2016). "A hybrid approach for de novo human genome sequence assembly and phasing". Nature Methods. 13 (7): 587–590. doi:10.1038/nmeth.3865
Linked-read_sequencing
Current calendar year
are concluded at the request of Pakistan. April 23 – Tornado outbreak sequence of April 23–28, 2026: An EF4 tornado hits the Vance Air Force Base in Enid
2026
DNA or RNA sequence that matches its complement when read backwards
A palindromic sequence is a nucleic acid sequence in a double-stranded DNA or RNA molecule whereby reading in a certain direction (e.g. 5' to 3') on one
Palindromic_sequence
Genome browser hosted by the University of California, Santa Cruz
LiftOver were introduced to enhance sequence alignment and coordinate conversion between different genome assemblies. Between 2004 and 2010, the UCSC Genome
UCSC_Genome_Browser
PMID 16020728. "TAIR - Genome Assembly". The Arabidopsis Genome Initiative (December 2000). "Analysis of the genome sequence of the flowering plant Arabidopsis
List of sequenced eukaryotic genomes
List_of_sequenced_eukaryotic_genomes
Application of computational algorithms, methods and programs to phylogenetic analyses
ancestral sequences. A comprehensive step-by-step protocol on constructing phylogenetic trees, including DNA/Amino Acid contiguous sequence assembly, multiple
Computational_phylogenetics
RNA family
occur in metagenomic sequences, and therefore might relate to problems with sequence assembly rather than biological sequences. The genes downstream
DinG_RNA_motif
RNA family
RNAs. However, the affected instances are in metagenomic sequences, where sequence assembly is often imperfect. Therefore, they could also reflect technical
Fibrobacter-1_RNA_motif
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SEQUENCE ASSEMBLY
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