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searching for Reference genome 183 found (247 total)

Cucurbita argyrosperma (1,078 words) [view diff] exact match in snippet view article find links to article

likely in the state of Jalisco, Mexico from its wild sororia form. The reference genome of this species was published in 2019. The flowers are orange or yellow

Salvinia (829 words) [view diff] exact match in snippet view article find links to article

abaxial. Salvinia cucullata is one of just two fern species for which a reference genome has been published. Small, floating aquatics with creeping stems, branched

Korean Bioinformation Center (544 words) [view diff] case mismatch in snippet view article find links to article

also been involved in the analysis for the Korean Reference Genome Project. The Korean Reference Genome Project was initiated by the then director Jong

N50, L50, and related statistics (1,550 words) [view diff] exact match in snippet view article find links to article

used. The U50 identifies unique, target-specific contigs by using a reference genome as baseline, aiming at circumventing some limitations that are inherent

End-sequence profiling (1,534 words) [view diff] exact match in snippet view article find links to article

to the reference genome. The differences, including orientation and length variations between constructed chromosomes and the reference genome, will suggest

Bacillus anthracis (4,674 words) [view diff] exact match in snippet view article find links to article

anthracis measures about 3 to 5 μm long and 1 to 1.2 μm wide. The reference genome consists of a 5,227,419 bp circular chromosome and two extrachromosomal

Nucleolus organizer region (762 words) [view diff] exact match in snippet view article find links to article

The exact sequence of these regions is not included in the human reference genome as of 2016 or the GRCh38.p10 released January 6, 2017. On 28 February

Azolla (2,709 words) [view diff] exact match in snippet view article find links to article

mosses. Azolla filiculoides is one of just two fern species for which a reference genome has been published. It is believed that this genus grew so prolifically

FASTQ format (3,618 words) [view diff] exact match in snippet view article find links to article

include DSRC and DSRC2, FQC, LFQC, Fqzcomp, and Slimfastq. Having a reference genome around is convenient because then instead of storing the nucleotide

SNV calling from NGS data (3,217 words) [view diff] exact match in snippet view article find links to article

NGS reads to remove sources of error/bias Aligning the reads to a reference genome Using an algorithm, either based on a statistical model or some heuristics

Digital transcriptome subtraction (1,428 words) [view diff] exact match in snippet view article find links to article

high-throughput sequencing and the availability of a high-quality, annotated reference genome of the host. The method specifically examines the etiological agent

Structural variation (3,555 words) [view diff] exact match in snippet view article find links to article

humans. While humans carry a median of 3.6 Mbp in SNPs (compared to a reference genome), a median of 8.9 Mbp is affected by structual variation which thus

Villoo Morawala-Patell (592 words) [view diff] exact match in snippet view article find links to article

the sequencing the first complete Zoroastrian-Parsi mitochondrial reference genome and genetic signatures of an endogamous non-smoking population with

Metatranscriptomics (4,188 words) [view diff] exact match in snippet view article find links to article

biased. A typical metatranscriptome analysis pipeline: maps reads to a reference genome, or performs de novo assembly of the reads into transcript contigs

Latrodectus elegans (426 words) [view diff] exact match in snippet view article find links to article

under-surveying of arachnids in this region. In 2022 a chromosome-scale reference genome was sequenced from specimens from Yunnan, producing a 1.57 Gb sized

HUGO Gene Nomenclature Committee (894 words) [view diff] exact match in snippet view article find links to article

2013). "Vive la différence: naming structural variants in the human reference genome". Human Genomics. 7 (1): 12. doi:10.1186/1479-7364-7-12. PMC 3648363

Computational genomics (1,977 words) [view diff] exact match in snippet view article find links to article

University published a genetic compression algorithm that does not use a reference genome for compression. HAPZIPPER was tailored for HapMap data and achieves

Avesthagen (1,742 words) [view diff] case mismatch in snippet view article find links to article

AGENOME-ZPMS-HV2a-1: The first complete Zoroastrian Parsi Mitochondrial Reference Genome In a new paper, available on bioRxiv in 2020, Avesthagen researchers

Eastern wolf (7,341 words) [view diff] exact match in snippet view article find links to article

relationships based on the only reference genome available: that of the dog breed called the Boxer. In 2017, the first reference genome of the wolf Canis lupus

Genome India Project (283 words) [view diff] exact match in snippet view article find links to article

gather samples, compile data, conduct research, and create an ‘Indian reference genome' grid. The initiative is funded by Department of Biotechnology (DBT)

PANTHER (2,612 words) [view diff] case mismatch in snippet view article find links to article

the function of gene products. PANTHER is part of the Gene Ontology Reference Genome Project designed to classify proteins and their genes for high-throughput

Oat (4,769 words) [view diff] exact match in snippet view article find links to article

traits has been hampered by the lack of a reference genome assembly. In May 2022, a fully annotated reference genome sequence of Avena sativa was reported

Deanna M. Church (307 words) [view diff] case mismatch in snippet view article find links to article

Brings Reference Genome Expertise to Personalis". Bio-itworld.com. Retrieved 6 December 2014. "A star is born: the updated Human Reference Genome". Blogs

SAMtools (1,396 words) [view diff] exact match in snippet view article find links to article

visualize how reads are aligned to specified small regions of the reference genome. Compared to a graphics based viewer like IGV, it has few features

De novo sequence assemblers (2,057 words) [view diff] exact match in snippet view article find links to article

assembles short nucleotide sequences into longer ones without the use of a reference genome. These are most commonly used in bioinformatic studies to assemble

List of sequence alignment software (2,355 words) [view diff] exact match in snippet view article find links to article

and uses a sequence database (EST, Sanger sequence) rather than a reference genome. BLAT Made by Jim Kent. Can handle one mismatch in initial alignment

Nyssa yunnanensis (391 words) [view diff] exact match in snippet view article find links to article

Higher Plants. To facilitate future conservation biology studies a reference genome was sequenced, creating a 1475 Mb assembly with 39,803 protein-coding

Aedes (992 words) [view diff] exact match in snippet view article find links to article

S, Antoshechkin I, Crawford JE, et al. (November 2018). "Improved reference genome of Aedes aegypti informs arbovirus vector control". Nature. 563 (7732):

Pileup format (575 words) [view diff] exact match in snippet view article find links to article

denotes a reference skip. This occurs, for example, if a base in the reference genome is intronic and a read maps to two flanking exons. If quality scores

Macadamia jansenii (423 words) [view diff] exact match in snippet view article find links to article

diversification of crop genetics to ensure food security, producing a 751 Mb reference genome assembled to 14 chromosomes. This is a potential model to study the

Genotyping by sequencing (842 words) [view diff] exact match in snippet view article find links to article

single-end reads. Raw sequence data are filtered and aligned to a reference genome using usually Burrows–Wheeler alignment tool (BWA) or Bowtie 2. The

Skink (2,741 words) [view diff] exact match in snippet view article find links to article

(Cryptoblepharus egeriae) was sequenced in 2022, representing the first skink reference genome. Skinks were long thought to have both genetic sex determination (GSD)

Korean Genome Project (728 words) [view diff] case mismatch in snippet view article find links to article

TheragenEtex to build the Variome of Koreans as well as the Korean Reference Genome (KOREF). Starting from KOREF, a consensus variome reference, providing

Portunus trituberculatus (645 words) [view diff] exact match in snippet view article find links to article

better understand the species development, evolution and reproduction a reference genome has been sequenced, assembling to 1.0 Gb in size and anchoring to 50

Coyote (15,878 words) [view diff] exact match in snippet view article find links to article

relationships based on the only reference genome available, that of the Boxer dog. In 2017, the first reference genome of the wolf Canis lupus lupus was

Zebrafish (11,740 words) [view diff] exact match in snippet view article find links to article

zebrafish reference genome revealed over 5 million single nucleotide variations and over 1.6 million insertion deletion variations. The zebrafish reference genome

Vicia sativa (1,676 words) [view diff] exact match in snippet view article find links to article

Iain R. (2021-10-13). "Chromosome-level assembly of the common vetch reference genome (Vicia sativa)": 2021.10.11.464017. doi:10.1101/2021.10.11.464017.

Red wolf (12,804 words) [view diff] exact match in snippet view article find links to article

relationships based on the only reference genome available, that of the Boxer dog. In 2017, the first reference genome of the wolf Canis lupus lupus was

Saccharomyces Genome Database (1,170 words) [view diff] exact match in snippet view article find links to article

biocuration is becoming more important for biomedical research. SGD keep reference genome sequence for the budding yeast S.cerevisiae. SGD are the source of

ATCC (company) (1,066 words) [view diff] exact match in snippet view article

began hosting the ATCC Genome Portal, a database of authenticated, reference genome assemblies and associated metadata for microbial strains held within

UCSC Genome Browser (1,641 words) [view diff] exact match in snippet view article find links to article

upload a file of their own data and view the data in the context of the reference genome assembly. Users may also use the data hosted by UCSC, creating subsets

Third-generation sequencing (3,988 words) [view diff] exact match in snippet view article find links to article

When a reference genome is available, as one is in the case of human, newly sequenced reads could simply be aligned to the reference genome in order

Dwarf cat (1,565 words) [view diff] exact match in snippet view article find links to article

dwarfism is being utilized in human research as well. Felis Catus 9.0, a reference genome for the cat, was utilized in research to analyze DNA of cats using

Human genetic variation (11,019 words) [view diff] exact match in snippet view article find links to article

2015, the typical difference between an individual's genome and the reference genome was estimated at 20 million base pairs (or 0.6% of the total). As of

Michael Ashburner (2,662 words) [view diff] case mismatch in snippet view article find links to article

PMID 17989687. Reference Genome Group of the Gene Ontology Consortium (2009). Bourne, Philip E. (ed.). "The Gene Ontology's Reference Genome Project: A Unified

Degradome sequencing (2,432 words) [view diff] exact match in snippet view article find links to article

be sequenced, and the results are compared with a transcriptome, or reference genome, in order to determine and characterize the abundance of the RNA fragments

Soursop (2,348 words) [view diff] exact match in snippet view article find links to article

Michael D.; Thomas, Daniel C.; Cao, Kunfang (2021). "Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research

Genome project (1,822 words) [view diff] case mismatch in snippet view article find links to article

Winston; Salzberg, Steven L; Neale, David B (November 1, 2020). "A Reference Genome Sequence for Giant Sequoia". G3: Genes, Genomes, Genetics. 10 (11):

Genome browser (1,633 words) [view diff] exact match in snippet view article find links to article

these complex data. Genome Assembly and Annotation: Give access to the reference genome assembly, serving as a framework for overlaying and analyzing other

Human Pangenome Reference (2,058 words) [view diff] exact match in snippet view article find links to article

pangenome seeks to address perceived shortcomings in the current human reference genome by offering a more comprehensive and inclusive resource for genomic

Transcriptome (4,861 words) [view diff] exact match in snippet view article find links to article

inferring transcriptome sequences. One approach maps sequence reads onto a reference genome, either of the organism itself (whose transcriptome is being studied)

Data compression (7,555 words) [view diff] exact match in snippet view article find links to article

University published a genetic compression algorithm that does not use a reference genome for compression. HAPZIPPER was tailored for HapMap data and achieves

Annona (1,695 words) [view diff] exact match in snippet view article find links to article

Michael D.; Thomas, Daniel C.; Cao, Kunfang (2021). "Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research

Indian cobra (4,895 words) [view diff] exact match in snippet view article find links to article

and emerging genomic technologies, a de novo high-quality N. naja reference genome was published in 2020. The estimated size of this haploid genome is

Australian ghostshark (1,104 words) [view diff] exact match in snippet view article find links to article

vertebrates, the Australian ghostshark genome will serve as a useful reference genome for understanding the origin and evolution of vertebrate genomes including

Tomato (10,126 words) [view diff] exact match in snippet view article find links to article

cultivar Heinz 1706 was published on 31 May 2012 in Nature. The latest reference genome published in 2021 had 799 MB and encodes 34,384 (predicted) proteins

Glomeromycota (2,016 words) [view diff] exact match in snippet view article find links to article

Johannesson, Hanna; Rosling, Anna (2020-01-28). "Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei"

List of sequenced animal genomes (27,644 words) [view diff] exact match in snippet view article find links to article

Pan Y, Tian M, Li Y, He C, et al. (April 2020). "Chromosome-level reference genome of the jellyfish Rhopilema esculentum". GigaScience. 9 (4). doi:10

Tripterygium wilfordii (1,166 words) [view diff] exact match in snippet view article find links to article

wilfordii. To aid the investigation of pathways related to celastrol, a reference genome of T. wilfordii was sequenced, producing a 340.12 Mb genome with 31

Chromosome 6 (2,420 words) [view diff] no match in snippet view article find links to article

transcription factor". T - T brachyury transcription factor - Genetics Home Reference. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs,

Hybrid genome assembly (2,951 words) [view diff] exact match in snippet view article find links to article

assembly is normally done by one of two methods: assembly using a reference genome as a scaffold, or de novo assembly. The scaffolding approach can be

Paired-end tag (1,846 words) [view diff] exact match in snippet view article find links to article

have reads that map further away than expected in the reference genome as the reference genome will have a segment of DNA that is not present in the sequenced

Bonobo (13,251 words) [view diff] exact match in snippet view article find links to article

While the first bonobo genome was published in 2012, a high-quality reference genome became available only in 2021. The overall nucleotide divergence between

History of research on Arabidopsis thaliana (5,679 words) [view diff] exact match in snippet view article find links to article

genetics. A. thaliana was the first plant for which a high-quality reference genome sequence was determined (see below), and a worldwide research community

Viral Bioinformatics Resource Center (1,542 words) [view diff] exact match in snippet view article find links to article

annotate a newly sequenced genome based on the annotations present in a reference genome; it can also predict new genes in the query genome. Bioinformatics

DNA methylation (13,166 words) [view diff] exact match in snippet view article find links to article

sequencing platform. The sequences obtained are then re-aligned to the reference genome to determine the methylation status of CpG dinucleotides based on mismatches

Biorepository (957 words) [view diff] case mismatch in snippet view article find links to article

and embedded in paraffin wax. The J. Craig Venter Institute Human Reference Genome makes available DNA samples from J. Craig Venter, whose genome has

Channel catfish (2,970 words) [view diff] exact match in snippet view article find links to article

fish species whose genomes have been sequenced. The channel catfish reference genome sequence was generated alongside genomic sequence data for other scaled

Single-cell DNA template strand sequencing (3,410 words) [view diff] exact match in snippet view article find links to article

applications for Strand-seq start by aligning sequenced reads to a reference genome. Alignment can be performed using a variety of short-read aligners

Papilio bianor (554 words) [view diff] exact match in snippet view article find links to article

X, Xie F, He J, Dong Z, et al. (November 2019). "Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation

Ciona (399 words) [view diff] case mismatch in snippet view article find links to article

Science, 298, 5601, S. 2157–67, 13. Dezember 2002 The C. savignyi Reference Genome and Genetic Map Sawada H, Morita M, Iwano M (August 2014). "Self/non-self

Structural variation in the human genome (3,756 words) [view diff] exact match in snippet view article find links to article

genetic variation. With improving sequencing technologies and the reference genome, more and more variations were found of several different sizes that

Aldabra giant tortoise (2,633 words) [view diff] exact match in snippet view article find links to article

reintroduction program by the Nature Protection Trust of Seychelles. A reference genome and low-coverage sequencing analyses has looked at revealing within-

SERPINA2 (1,045 words) [view diff] exact match in snippet view article find links to article

a functional protein. This gene may be an evolving pseudogene. The reference genome contains the start codon mutation and has a coding region deletion

Trifoliate orange (1,808 words) [view diff] exact match in snippet view article find links to article

Gmitter, Frederick G. Jr; Deng, Zhanao (2020). "A chromosome‐scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease

Pontederia crassipes (9,434 words) [view diff] exact match in snippet view article find links to article

was introduced into the area in the 1980s. A 1.22 Gb/8 chromosome reference genome was assembled to study nuclear and chloroplast genomes between 10 water

Paddlefish (3,030 words) [view diff] no match in snippet view article find links to article

Paddlefish--A Representative Basal Ray-Finned Fish and Important Comparative Reference". Genome Biology and Evolution. 4 (9): 937–953. doi:10.1093/gbe/evs067. PMC 3509897

Retrotransposon (3,103 words) [view diff] exact match in snippet view article find links to article

between individuals. There is an estimate of 80–100 active L1s in the reference genome of the Human Genome Project, and an even smaller number of L1s within

Proboscipedia (fly gene) (248 words) [view diff] exact match in snippet view article

2015). "FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations". Nucleic

Balamuthia mandrillaris (2,030 words) [view diff] exact match in snippet view article find links to article

encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing". Genome Medicine. 7 (1): 113. doi:10.1186/s13073-015-0235-2

List of RNA-Seq bioinformatics tools (20,371 words) [view diff] exact match in snippet view article find links to article

of RNA-Seq analysis involves alignment of the sequenced reads to a reference genome (if available) or to a transcriptome database. See also List of sequence

Biomphalaria straminea (667 words) [view diff] exact match in snippet view article find links to article

accompanying transcriptomes has been sequenced, producing a 1.005 Gb in size reference genome consisting of 36 chromosomes. A cladogram showing phylogenic relations

DNA sequencer (3,850 words) [view diff] exact match in snippet view article find links to article

isoform variant detection. GS Reference Mapper maps short reads to a reference genome, generating a consensus sequence. The software is able to generate

List of sequenced plant genomes (10,505 words) [view diff] exact match in snippet view article find links to article

LW, Couvreur TL, Erkens RH, et al. (July 2021). "Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research

Pig (8,573 words) [view diff] exact match in snippet view article find links to article

H.; Bickhart, D. M.; Billis, K.; et al. (2020). "An improved pig reference genome sequence to enable pig genetics and genomics research". GigaScience

Sugar beet (5,278 words) [view diff] exact match in snippet view article find links to article

super-Caryophyllales and at or sub-Eudicots. It has been sequenced and two reference genome sequences have already been generated. The genome size of the sugar

1q21.1 deletion syndrome (2,681 words) [view diff] exact match in snippet view article find links to article

heterozygous deletion within the position of 145-146.35 Mb in the reference genome confirms the diagnosis of 1q21.1 deletion. The copy number of sequences

Sanger sequencing (3,257 words) [view diff] exact match in snippet view article find links to article

long-read sequencing and assembly extends the Caenorhabditis elegans reference genome". Genome Research. 28 (2): 266–274. doi:10.1101/gr.221184.117. PMC 5793790

1996 in science (2,420 words) [view diff] case mismatch in snippet view article find links to article

Miyasato, Stuart R.; Simison, Matt; Cherry, J. Michael (2014). "The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now". G3. 4 (3): 389–398

Aquaculture of tilapia (2,795 words) [view diff] exact match in snippet view article find links to article

placed at a chromosome level as the karyotype was already known. The reference genome also has the non-nuclear mitochondrial genome. With help from bioinformatics

Earth BioGenome Project (721 words) [view diff] case mismatch in snippet view article find links to article

(i5k) Project Website The Bird 10,000 Genomes (B10K) Project Website The Darwin Tree of Life Website The European Reference Genome Atlas (ERGA) Website

Limnodynastes dumerilii (987 words) [view diff] exact match in snippet view article find links to article

rain. The Eastern banjo frog was the first of the species to have its reference genome sequenced, finding a compact (for an amphibian) 2.38 Gb genome and

MPEG-G (1,074 words) [view diff] exact match in snippet view article find links to article

annotations — that is, a number of heterogeneous data types associated with intervals of the reference genome that the sequencing data has been aligned to.

WI-38 (969 words) [view diff] exact match in snippet view article find links to article

therefore a good model for genome sequencing and serves as another reference genome. Use of fetal tissue in vaccine development MRC-5 "WI-38 (ATCC® CCL-75™)"

ChIP sequencing (3,353 words) [view diff] exact match in snippet view article find links to article

as they are not informative and may interfere with mapping in the reference genome. Fragments in peaks: ratio of reads that are located in peaks over

Non-coding DNA (4,778 words) [view diff] exact match in snippet view article find links to article

1016/j.cell.2020.09.014. PMC 7541718. PMID 32976797. "Ensemble Human reference genome GRCh38.p13". Xu J, Zhang J (2015). "Are human translated pseudogenes

Catherine Feuillet (2,133 words) [view diff] exact match in snippet view article find links to article

physical maps of each individual chromosome and sequence them to get to a reference genome sequence. At that time whole genome sequencing approaches did not yield

Ötzi (8,299 words) [view diff] exact match in snippet view article find links to article

July 2013). "Scalable metagenomic taxonomy classification using a reference genome database". Bioinformatics. 29 (18): 2253–2260. doi:10.1093/bioinformatics/btt389

Colossal Biosciences (2,397 words) [view diff] exact match in snippet view article find links to article

Vertebrate Genomes Project to successfully generate the first high-quality reference genome of an African elephant. This sequencing work is part of a long-term

Sequence assembly (2,625 words) [view diff] exact match in snippet view article find links to article

PMID 20211242. Wolf, Beat. "De novo genome assembly versus mapping to a reference genome" (PDF). University of Applied Sciences Western Switzerland. Retrieved

Genomics (7,518 words) [view diff] exact match in snippet view article find links to article

Paired end reads of next generation sequencing data mapped to a reference genome.

Medicinal plants (8,377 words) [view diff] case mismatch in snippet view article find links to article

Berries Is Conferred Primarily by Genes That Are Not Shared with the Reference Genome". The Plant Cell. 25 (12): 4777–4788. doi:10.1105/tpc.113.118810. JSTOR 43190600

Parsis (11,428 words) [view diff] case mismatch in snippet view article find links to article

(June 8, 2020). "The First complete Zoroastrian-Parsi Mitochondria Reference Genome: Implications of mitochondrial signatures in an endogamous, non-smoking

Gene expression (9,242 words) [view diff] exact match in snippet view article find links to article

producing vast quantities of sequence data that can be matched to a reference genome. Although NGS is comparatively time-consuming, expensive, and resource-intensive

Sorghum (4,218 words) [view diff] exact match in snippet view article find links to article

D.; McKinley, Brian; Mattison, Ashley (2018). "The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures

DNA microarray (5,427 words) [view diff] exact match in snippet view article find links to article

characterize and quantify gene expression. Unlike microarrays, which need a reference genome and transcriptome to be available before the microarray itself can

Vaquita (4,679 words) [view diff] exact match in snippet view article find links to article

Jennifer R.; et al. (May 2021) [First published: 22 October 2020]. "Reference genome and demographic history of the most endangered marine mammal, the vaquita"

Burrows–Wheeler transform (3,463 words) [view diff] exact match in snippet view article find links to article

experiments, e.g., in ChIP-Seq, the task is now to align these reads to a reference genome, i.e., to the known, nearly complete sequence of the organism in question

Vaquita (4,679 words) [view diff] exact match in snippet view article find links to article

Jennifer R.; et al. (May 2021) [First published: 22 October 2020]. "Reference genome and demographic history of the most endangered marine mammal, the vaquita"

Transposable element (7,362 words) [view diff] exact match in snippet view article find links to article

Liang T, Stitzer MC, Wang B, et al. (June 2017). "Improved maize reference genome with single-molecule technologies". Nature. 546 (7659): 524–527. Bibcode:2017Natur

Sequoiadendron giganteum (7,771 words) [view diff] case mismatch in snippet view article find links to article

Winston; Salzberg, Steven L; Neale, David B (November 1, 2020). "A Reference Genome Sequence for Giant Sequoia". G3: Genes, Genomes, Genetics. 10 (11):

Cryptoblepharus egeriae (1,082 words) [view diff] exact match in snippet view article find links to article

gecko) was sequenced in 2022, marking the first high quality skink reference genome. Analysis of this genome revealed high genetic diversity, reflective

Coconut (16,198 words) [view diff] exact match in snippet view article find links to article

Muhammad Tahir ul; Xia, Wei; Liu, Rui (November 4, 2021). "High-quality reference genome sequences of two coconut cultivars provide insights into evolution

Mutation (13,965 words) [view diff] exact match in snippet view article find links to article

important contextual factors to our evolution. Compared to the human reference genome, a typical human genome varies at approximately 4.1 to 5.0 million

Zonadhesin (343 words) [view diff] exact match in snippet view article find links to article

this gene results in both functional and frameshifted alleles; the reference genome represents the functional allele. Alternative splicing of this gene

Venturia effusa (254 words) [view diff] exact match in snippet view article find links to article

Clive H.; Cox, Murray P.; Young, Carolyn A. (2020). "Chromosome-level reference genome of Venturia effusa, causative agent of pecan scab". Molecular Plant-Microbe

Personalized medicine (9,261 words) [view diff] exact match in snippet view article find links to article

individual's DNA sequence, their genome can then be compared to a reference genome, like that of the Human Genome Project, to assess the existing genetic

Julian Parkhill (2,203 words) [view diff] exact match in snippet view article find links to article

reads: Julian Parkhill has played a major role in determining the reference genome sequences of many key bacterial pathogens, including Mycobacterium

Haemonchus contortus (1,663 words) [view diff] exact match in snippet view article find links to article

contortus draft genome was published in 2013. Further work to complete the reference genome is underway at the Wellcome Trust Sanger Institute in collaboration

Craig Venter (5,957 words) [view diff] case mismatch in snippet view article find links to article

first haplotype-resolved human genomes began to appear. The Human Reference Genome Browser is a web application for the navigation and analysis of Venter's

Bif2 barren inflorescence2 (598 words) [view diff] exact match in snippet view article find links to article

RFLP marker umc67a (McSteen and Hake 2001) and the 2010 B73_v2 maize reference genome sequence assembly. Genetically mapped SNPs near the gene include rs131816257

Arabidopsis thaliana (8,632 words) [view diff] exact match in snippet view article find links to article

(2017). "Araport11: a complete reannotation of the Arabidopsis thaliana reference genome". The Plant Journal. 89 (4): 789–804. doi:10.1111/tpj.13415. ISSN 1365-313X

Hepatitis D (5,940 words) [view diff] exact match in snippet view article find links to article

situation which has been resolved recently with the adoption of a proposed reference genome and a uniform classification system. Like hepatitis B, HDV gains entry

Superb fairywren (4,333 words) [view diff] exact match in snippet view article find links to article

superfamily Meliphagoidea. To help resolve this a high-quality 1.07‐Gb reference genome was sequenced in 2019. Six subspecies are currently recognized: M.

Cap analysis of gene expression (1,287 words) [view diff] exact match in snippet view article find links to article

quantification of the RNA transcript abundances in biological samples. Using a reference genome, a researcher can usually determine, with some confidence, the original

Metagenomics (9,198 words) [view diff] exact match in snippet view article find links to article

With the mOTUs profiler is possible to profile species without a reference genome, improving the estimation of microbial community diversity. Recent

Siamese fighting fish (10,385 words) [view diff] exact match in snippet view article find links to article

Ren, Zhitao; Xu, Qiwu; Liu, Qun (11 July 2018). "Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the

Western honey bee (11,408 words) [view diff] exact match in snippet view article find links to article

multiple pieces called scaffolds. The existence of a highly contiguous reference genome for a species enables more detailed investigations of evolutionary

Citrus taxonomy (8,059 words) [view diff] exact match in snippet view article find links to article

Gmitter, Frederick G. Jr.; Deng, Zhanao (2020). "A chromosome-scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease

Glossary of cellular and molecular biology (0–L) (24,805 words) [view diff] exact match in snippet view article

genes within human cells, and ultimately of assembling a complete reference genome for the human species. The project was launched in 1990 by a consortium

Optical mapping (2,102 words) [view diff] exact match in snippet view article find links to article

nanocoding have been developed to align single-molecule barcodes with a reference genome. Multiple sequence reads from the same large template molecule. These

Rat Genome Database (4,150 words) [view diff] exact match in snippet view article find links to article

descendant of the female BN rat previously sequenced. The new BN rat reference genome was created using a variety of technologies including PacBio long reads

Wang Jian (geneticist) (670 words) [view diff] exact match in snippet view article

was involved in the sequencing of the rice genome, first Asian human reference genome and numerous other large-scale genomics projects. In 2003 he was involved

Epigenomics (5,663 words) [view diff] exact match in snippet view article find links to article

histones, or those that are not. These sequences are then compared to a reference genome that allows to identify their relative position. MNase-seq and DNase-seq

FAIRE-Seq (1,541 words) [view diff] exact match in snippet view article find links to article

sensitive method. In a first step FAIRE-seq data are mapped to the reference genome of the model organism used. Next, the identification of genomic regions

Cuneiform (programming language) (1,834 words) [view diff] exact match in snippet view article

streamlined but similar version. The following example script downloads a reference genome from an FTP server. declare download-ref-genome; deftask download-fa(

UC Santa Cruz Genomics Institute (1,046 words) [view diff] exact match in snippet view article find links to article

Human Genome Reference Program to create a more complete and diverse reference genome. One of the institute's Associate Directors, Karen Miga, recently co-led

Comparative genomics (8,127 words) [view diff] exact match in snippet view article find links to article

and deletions by mapping unassembled reads against a well annotated reference genome, and thus provide a list of possible gene differences that may be the

Bacillus firmus (930 words) [view diff] exact match in snippet view article find links to article

this strain in 2014 and the sequencing of its genome, there was no reference genome sequence available, despite B. firmus’s wide use as a controller of

Venturia (fungus) (1,741 words) [view diff] exact match in snippet view article

Clive H.; Cox, Murray P.; Young, Carolyn A. (2020). "Chromosome-level reference genome of Venturia effusa, causative agent of pecan scab". Molecular Plant-Microbe

Mycoplasma laboratorium (3,641 words) [view diff] exact match in snippet view article find links to article

differences are present in Mycoplasma mycoides JCVI-syn1.0 relative to the reference genome, notably an E.coli transposon IS1 (an infection from the 10kb stage)

BGI Group (5,150 words) [view diff] exact match in snippet view article find links to article

(identifying an eight kilobase insertion not detected by mapping to the human reference genome) and animals, like the giant panda. Up until 2015, BGI had released

Comparative genomic hybridization (5,284 words) [view diff] exact match in snippet view article find links to article

high-resolution scale. Array CGH compares the patient's genome against a reference genome and identifies differences between the two genomes, and hence locates

SPAdes (software) (2,236 words) [view diff] exact match in snippet view article

size is used rather than the assembly size). Moreover, using E. coli reference genome, SPAdes assembled the highest percentage of genome (97%) and the highest

Haplogroup R-Z18 (668 words) [view diff] exact match in snippet view article find links to article

haplogroups in populations of Europe This position is with respect to human reference genome assembly GRCh37/hg19 released on March 7, 2009 by the Genome Reference

Endocrine disruptor (16,616 words) [view diff] exact match in snippet view article find links to article

Torrance J, Berthelot C, Muffato M, et al. (April 2013). "The zebrafish reference genome sequence and its relationship to the human genome". Nature. 496 (7446):

Linked-read sequencing (2,569 words) [view diff] exact match in snippet view article find links to article

on barcodes. Downstream Analysis: processed reads are aligned to a reference genome, or used for de novo assembly of complex genomes, haplotype phasing

Micromonas (2,868 words) [view diff] exact match in snippet view article find links to article

specifically land plants and chlorophyte green algae. The original Micromonas reference genome(s) were created from strain CCMP1545 isolated from the North Atlantic

Arbuscular mycorrhiza (11,430 words) [view diff] exact match in snippet view article find links to article

Johannesson, Hanna; Rosling, Anna (2020-01-28). "Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei"

CUT&RUN sequencing (2,049 words) [view diff] exact match in snippet view article find links to article

the Motif Alignment and Search Tool (MAST) to identify motifs in a reference genome that match the acquired sequence reads. This process allows the identification

Single-cell transcriptomics (3,625 words) [view diff] exact match in snippet view article find links to article

generation sequencing techniques and the reads are mapped back to the reference genome, providing a count of the number of reads associated with each gene

Podospora anserina (2,528 words) [view diff] exact match in snippet view article find links to article

strains are known to be very similar except for the het-s locus. The reference genome published in 2008 corresponds to S+, a haploid derivate of the S strain

CITE-Seq (2,326 words) [view diff] exact match in snippet view article find links to article

standard scRNA-Seq experiment. Firstly, reads need to be aligned to a reference genome of a species of interest and cells with very low number of transcripts

Rajeev Kumar Varshney (4,853 words) [view diff] exact match in snippet view article find links to article

made significant scientific contributions including the following: Reference genome sequence assemblies for 13 plant species: namely pigeonpea, chickpea

Luca Comai (1,261 words) [view diff] exact match in snippet view article find links to article

developed in 2004, to compare differences in these plant lines to the reference genome and isolate new mutations and traits for further research. He would

Jumping library (2,917 words) [view diff] exact match in snippet view article find links to article

generated, but only 11.6% of these could be mapped uniquely to the reference genome, which represents approximately a sixfold coverage. Talkowski et al

Reduced representation bisulfite sequencing (1,812 words) [view diff] exact match in snippet view article find links to article

available, such as Maq, BS Seeker, Bismark or BSMAP. Alignment to a reference genome allows the programs to identify base pairs within the genome that are

Methylated DNA immunoprecipitation (2,851 words) [view diff] exact match in snippet view article find links to article

bp, depending on the technology). The short reads are aligned to a reference genome using alignment software such as Mapping and Assembly with Quality

G-value paradox (1,906 words) [view diff] exact match in snippet view article find links to article

Torrance J, Berthelot C, Muffato M, et al. (April 2013). "The zebrafish reference genome sequence and its relationship to the human genome". Nature. 496 (7446):

Phormia regina (4,251 words) [view diff] exact match in snippet view article find links to article

entire genome of P. regina has been sequenced so that it may serve as a reference genome that can be used in comparison with other Calliphoridae species. This

BBSome (6,786 words) [view diff] exact match in snippet view article find links to article

underwent high throughput sequencing, were aligned with the human reference genome, and single nucleotide polymorphism calling was performed. Approximately

Glossary of cellular and molecular biology (M–Z) (21,825 words) [view diff] exact match in snippet view article

adenine (A). SNPs are usually defined with respect to a "standard" reference genome; an individual human genome differs from the reference human genome

DeCODE genetics (9,735 words) [view diff] exact match in snippet view article find links to article

chromosomes. The map was critical to correcting and completing the public reference genome sequence in 2003, improving the accuracy of the HGP assembly from 93%

Whole genome bisulfite sequencing (2,517 words) [view diff] exact match in snippet view article find links to article

methylation profile. One such study aligns the new reads against the reference genome in order to directly compare locations of methylated cytosines and

FAM166C (1,605 words) [view diff] exact match in snippet view article find links to article

associated with periodontitis. Using whole exome sequencing and the human reference genome as a comparison, a novel FAM166C SNP was identified as the only gene

Source attribution (14,501 words) [view diff] exact match in snippet view article find links to article

fragments (short reads). Alternatively, short reads can be mapped to a reference genome sequence that has been converted into an index for efficient lookup

Perturb-seq (2,588 words) [view diff] exact match in snippet view article find links to article

Read alignment and processing are performed to map quality reads to a reference genome. Deconvolution of cell barcodes, guide barcodes and UMIs enables the

SPT20 (403 words) [view diff] exact match in snippet view article find links to article

Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M. (2014): The reference genome sequence of Saccharomyces cerevisiae: Then and now. G3 (Bethesda) 4:389-398(2014)

Small RNA sequencing (2,056 words) [view diff] exact match in snippet view article find links to article

the sequencing process); reads can then be mapped or aligned to a reference genome in order to extract information about their similarity: reads having

TBC1D30 (1,160 words) [view diff] exact match in snippet view article find links to article

the genome build. The first three in the list are independent of the reference genome. The latter 6, labelled with an X, are based on NC_000012.12 Reference

Off-target genome editing (6,822 words) [view diff] exact match in snippet view article find links to article

expensive and like exome sequencing, whole genome also requires a reference genome to make inferences. BLESS is the easiest way to detect and quantify

Gene Disease Database (4,122 words) [view diff] exact match in snippet view article find links to article

the effects of variants. For each variation that is mapped to the reference genome, each Ensembl transcript is identified that overlap the variation.

Beat Keller (1,534 words) [view diff] exact match in snippet view article find links to article

Stein, N. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361: eaar7191. DOI:10.1126/science.aar7191

Cellular deconvolution (3,545 words) [view diff] no match in snippet view article find links to article

composition from DNA methylation without the need for methylation reference". Genome Biology. 19 (1): 141. doi:10.1186/s13059-018-1513-2. PMC 6151042.

Hi-C (genomic analysis technique) (10,971 words) [view diff] exact match in snippet view article

data analysis. Paired-end reads are first iteratively mapped to a reference genome. Mapped reads are then assigned to a restriction fragment/genomic loci

List of inventions and discoveries by women (7,595 words) [view diff] exact match in snippet view article find links to article

Michael S.; Stein, Joshua C.; Wei, Xuehong (2017-06-22). "Improved maize reference genome with single-molecule technologies". Nature. 546 (7659): 524–527. Bibcode:2017Natur

Solynta (2,198 words) [view diff] case mismatch in snippet view article find links to article

Finkers, Richard (October 2020). "Solyntus, the New Highly Contiguous Reference Genome for Potato ( Solanum tuberosum )". G3: Genes, Genomes, Genetics. 10

Genome skimming (4,505 words) [view diff] exact match in snippet view article find links to article

alignment-free tool to compute genomic distances between the query and reference genome skims. Skmer uses a 2 stage approach to compute these distances. First

Pore-C (1,989 words) [view diff] exact match in snippet view article find links to article

from different regions of the genome, aligning sequencing reads to a reference genome is challenging. One solution to this problem involves a bioinformatic

Neurogenomics (9,520 words) [view diff] exact match in snippet view article find links to article

contingent on the availability of a fully sequenced and annotated reference genome. Additionally, the RNA profiles (miRNA, ncRNA, mRNA) of the model organism

Ancient pathogen genomics (5,940 words) [view diff] exact match in snippet view article find links to article

distance should be chosen according to the phylogenetic distance to the reference genome. Probabilistic aligners that take into account the damage pattern of

Nicrophorus pustulatus (8,431 words) [view diff] exact match in snippet view article find links to article

the whole genome or individual chromosomes are currently available. Reference genome sequences are available for other members of the genus, including reference

Circular consensus sequencing (3,074 words) [view diff] exact match in snippet view article find links to article

Sauria, Michael E. G.; Vollger, Mitchell R. (2022-04-01). "A complete reference genome improves analysis of human genetic variation". Science. 376 (6588):