Markers for molecular contig mapping. Medical search. Frequent questions

Gene mapping or genome mapping describes the methods used to identify the location of a gene on a chromosome and the distances between genes. (wikipedia.org)
Genes can be viewed as one special type of genetic markers in the construction of genome maps, and mapped the same way as any other markers. (wikipedia.org)
Gene maps help describe the spatial arrangement of genes on a chromosome. (wikipedia.org)
Genes are designated to a specific location on a chromosome known as the locus and can be used as molecular markers to find the distance between other genes on a chromosome. (wikipedia.org)
A gene map helps point out the relative positions of genes and allows researchers to locate regions of interest in the genome. (wikipedia.org)
Genetic mapping on the other hand uses genetic techniques to indirectly find association between genes. (wikipedia.org)
These technique allow for maps to be constructed so that relative positions of genes and other important sequences can be analyzed. (wikipedia.org)
The numerous microsatellites will facilitate integration of the linkage and physical maps and serve as valuable resource for fine mapping QTL and positional cloning of genes affecting aquaculture production traits. (biomedcentral.com)
Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)
We have contributed to the assembly process by mapping markers/genes to BACs and contigs using overgo hybridization. (kent.ac.uk)
Analysis is in progress to map these loci and identify the genes responsible for the retinal degeneration phenotype in these mutant lines. (zfin.org)
Comparative studies of phylogenetic trees based on genome-wide SNPs showed that the genome-wide SNP tree generated in this study differed from the one based on insertion point markers and selected SNPs in the mutT and ogt genes by having the evolutionary positions of sub-lineages 5 and 6 interchanged. (sun.ac.za)
Of the 155 markers present in the two contigs, 141 (33 genes and 108 STS) were generated and mapped in this study. (uaeu.ac.ae)
Considering limited representation of the region in the latest version of the horse whole genome sequence EquCab2, the dense map developed in this study will prove useful for the assembly and annotation of the sequence data on ECA21 and will be instrumental in rapid search and isolation of candidate genes for traits mapped to this region. (uaeu.ac.ae)
Full genome-sequencing of additional species and specimens of S. haematobium, S. japonicum, and S. mansoni is desirable to better characterize differences within and among these species, to develop additional genetic markers, and to examine genes as well as conserved non-coding elements associated with drug resistance. (biomedcentral.com)
And when we started mapping these active promoter genes, we found that in addition to thousands of signals at sites of known genes, many signals are mapped to different genomic sites where no genes are marked by the reference genome. (vechnayamolodost.ru)
Our study contains an extensive sequencing and functional gene-annotation analysis of A. sativum L. The findings provide insights into the molecular basis of TFs, defensive genes, and a reference for future studies on the genetics and breeding of A. sativum L. (springeropen.com)
RNA sequencing has been used for the genome-wide quantification of absolute transcript levels, the identification of novel genes, the characterization of transcript structure (including 50 and 30 ends, introns, and exons), and the mining of molecular markers. (springeropen.com)
The above-mentioned ab, of repetitive sequences in plant genomes (up to 99%), makes difﬁcult the application of this technique for, mapping individual plant genes [40]. (centrocardiobogota.com)

While the physical map could be a more accurate representation of the genome, genetic maps often offer insights into the nature of different regions of the chromosome, for example the genetic distance to physical distance ratio varies greatly at different genomic regions which reflects different recombination rates, and such rate is often indicative of euchromatic (usually gene-rich) vs heterochromatic (usually gene-poor) regions of the genome. (wikipedia.org)
The closer two markers are on the chromosome, the more likely they are to be passed on to the next generation together. (wikipedia.org)
In this study, we constructed the first comprehensive physical map of wheat chromosome arm 5DS, thereby exploring its gene space organization and evolution. (biomedcentral.com)
Ordering of 80 contigs along the deletion bins of chromosome arm 5DS revealed small-scale breaks in syntenic blocks. (biomedcentral.com)
DNA probes from DXS732 and DXS453, identified as the closest flanking marker loci to the EDA locus, were used to identify homologous Yeast Artificial Chromosome (YAC) clones. (ox.ac.uk)
A bacterial artificial chromosome (BAC) library was constructed from high molecular weight DNA of HR45 and is composed of 33,024 clones. (tamu.edu)
A long range deletion map was constructed using available X chromosome YAC contigs and the DNA of the proband of family 1, hybrid 1C3 derived from the mother of family 2, and patients 3 and 4. (bmj.com)
To facilitate M. grisea genome analysis, physical mapping, and positional cloning, we have constructed a bacterial artificial chromosome (BAC) library from the rice infecting strain 70-15. (johnshopkins.edu)
In addition, a 550-kbp contig composed of 6 BAC clones was constructed that encompassed two adjacent RFLP markers on chromosome 2. (johnshopkins.edu)
We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. (biomedcentral.com)
A total of 207 BAC clones containing 155 loci were isolated and arranged into a map of linearly ordered overlapping clones over the proximal part of horse chromosome 21 (ECA21), which corresponds to the proximal half of the short arm of human chromosome 19 (HSA19p) and part of HSA5. (uaeu.ac.ae)
gene is mapped on the wheat chromosome 5B, but, neither obtaining a physical marker nor microdissec-, tion of this chromosomal region gave practical results, [56]. (centrocardiobogota.com)

5 clones) that constitute ~95 % of the cumulative length of the map. (biomedcentral.com)
Direct cosmid-cosmid hybridisation analysis placed subsets of these clones within four different cosmid contigs. (ox.ac.uk)
Mapping of anchor clones from each contig, against the mapping panel, localised all these contigs within the Xq12-q13.1 region. (ox.ac.uk)
To facilitate this integration of maps, we screened 3290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the 'Williams 82' physical map. (arizona.edu)
Two to seven BAC clones were identified by each marker. (tamu.edu)
Two clones were found to have both markers PV-tttc001 and STS183. (tamu.edu)
One preliminary contig was assembled based on DNA finger printing of those positive BAC clones. (tamu.edu)
The minimum tiling path of the contig contains 6 BAC clones spanning an estimated size of 750 kb covering the QTL region. (tamu.edu)
The clones form two contigs - each corresponding to the respective human chromosomes - that are estimated to be separated by a gap of ∼200 kb. (uaeu.ac.ae)

1 The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA. (nih.gov)
Part of the research focus is directed toward developing marker assisted breeding protocols for the breeding program, therefore I conduct basic and applied research on apple genetics, particularly in the area of disease resistance, root and tree architecture, rootstock mediated plant nutrition and dwarfing mechanisms of apple rootstocks. (usda.gov)
It provides genetic markers for investigating the taxonomy, population genetics, and phylogenetics of pinworms from different hosts and has implications for the diagnosis, prevention, and control of parasitic diseases in porcupines and other animals. (nature.com)

The most common sample used in gene mapping, especially in personal genomic tests is saliva. (wikipedia.org)
Genomic organization was determined by alignment of contigs with published cDNA sequences and zebrafish genomic sequence from Sanger and Ensembl databases. (zfin.org)
The newly identified structural variants will facilitate genetic improvement of tomato through both marker-assisted selection and genomic selection. (nature.com)
OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps. (cdc.gov)
These data provide a foundational map of large SV in the morbid human genome and demonstrate a previously underappreciated abundance and diversity of cxSV that should be considered in genomic studies of human disease. (biomedcentral.com)
Since 2001, the composition of the genome has been updated several times, most recently in 2019?Yes, but there were still pieces of genomic DNA sequences that could not be "stuck" into the whole sequence, into the contig. (vechnayamolodost.ru)

Overgo hybridization provides a cost-effective, high throughput method for integration of physical maps, sequences and linkage maps for many species, including other avians. (kent.ac.uk)

Physical mapping utilizes molecular biology techniques to inspect chromosomes. (wikipedia.org)
The application of molecular biology to the answering of epidemiological questions. (bvsalud.org)

Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. (nih.gov)
Reliable contigs are analysed with our software Full-LengtherNext to discard non-coding sequences, split chimeras, detect transcripts containing complete proteins, provide an overview of the transcriptome, and sort putative new or species-specific transcripts. (uma.es)
Moreover, SL5.0 contains 19.3 Mb more sequences than SL4.0 (801.8 Mb versus 782.5 Mb), with 43 contigs (99.8% of the assembly) ordered and oriented on the 12 chromosomes (Fig. 1a and Extended Data Fig. 2b ). (nature.com)
Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma species (i.e., using DNA sequences conserved among species) , as well as other markers that are specific to species or species-groups (i.e., using DNA sequences that differ among species). (biomedcentral.com)
Recent molecular analyses of mt genome sequences have provided selectable hypotheses for the phylogenetic relationships of nematodes based on 18S rRNA. (nature.com)
The sequences also show an The conventional and marker-assisted breeding (MAB) are the two approaches used to accomplish plant breeding (Breseghello and Coelho, 2013). (centrocardiobogota.com)

These techniques consequently allow researchers to observe chromosomes directly so that a map may be constructed with relative gene positions. (wikipedia.org)
The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary relationships, provides tools for map-based cloning, and serves as a framework for reference sequencing efforts. (biomedcentral.com)
A panel of somatic cell hybrids and X-linked hypohidrotic ectodermal dysplasia (EDA) patient-derived cell lines, containing different rearranged X chromosomes, have been used to refine the physical map of the Xq12-q13.1 region. (ox.ac.uk)
We've assigned over 6000 BACs to over 600 markers across almost all chicken chromosomes and linkage groups. (kent.ac.uk)
Dual color fluorescence in situ hybridization on metaphase and interphase chromosomes verified the relative order of some of the BACs and helped to orient them accurately in the contigs. (uaeu.ac.ae)
We used high-throughput chromatin conformation capture (Hi-C) and Proximity-Guided Assembly (PGA) to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes. (oregonstate.edu)
The seven pseudo-chromosomes cover ~97.2% of the total contig length (~223.8 Mb). (oregonstate.edu)
results can serve as an important argument in favour of the proposal to develop a special program for sequencing the genome chromosomes and for, To estimate the possibility of plant genome mapping using human genome probes, the probes fluorescent in situ hybridization (FISH) of human 18S-28S rDNA (clon 22F9 from the LA-13NCO1 library) was carried out on chromosomes of the spring barleyHordeum vulgareL. (centrocardiobogota.com)

Predicted CDS were compared to the databases InterPro ( 18 ), Swissprot ( 19 ), and trEMBL ( 19 ) for functional annotation and mapped to KEGG pathways. (asm.org)

BAC fingerprint analyses and alignments of BACs to the pre-existing linkage map have generated a BAC contig physical map of the genome. (kent.ac.uk)
One hundred and ten originated in BACs located in contigs for which no genetic map location was previously known. (arizona.edu)
Ninety-five SSRs came from BACs within contigs for which one or more other BACs had already been mapped. (arizona.edu)

In this study, the D locus was mapped to a 509-kb interval, with two markers, 5dC720 and 5C1019, co-segregating with the non-acid/acid trait of peach fruit. (bvsalud.org)

While both maps are a collection of genetic markers and gene loci, genetic maps' distances are based on the genetic linkage information, while physical maps use actual physical distances usually measured in number of base pairs. (wikipedia.org)
Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium . (biomedcentral.com)
About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. (biomedcentral.com)

The latter markers were however more appropriate for molecular epidemiology studies. (sun.ac.za)
In its broad context, genetic epidemiology includes family studies, molecular epidemiologic studies with genetic components, and more traditional cohort and case-control studies with family history components. (bvsalud.org)

The high-quality physical map constructed in this study paves the way for the assembly of a reference sequence, from which breeding efforts will greatly benefit. (biomedcentral.com)
Algorithms and filters used to improve the Tribolium draft Assembly with Physical Maps Based on Imaging Ultra-Long Single DNA Molecules. (slideshare.net)
A strategy is introduced by which physical and genetic map inconsistencies can be resolved using the preliminary 4x assembly of the whole genome sequence of soybean. (arizona.edu)
Following alignment of unmapped reads to each minicircle contig, we assessed the quality of the minicircle assembly by calculating the number of mapped reads, properly paired reads and the proportion of properly paired reads containing the Conserved Sequence Block 3 (CSB3) (i.e. a highly conserved 12-mer within the minicircle). (howest.be)

Putative microsatellite and SNP markers were identified. (nih.gov)
Finally, descriptions, GO, InterPro, KEGG and EC codes are added using Sma3 and AutoFact, and a set of microsatellite markers is obtained with MREPS. (uma.es)
Pseudomolecules as well as unmapped scaffolds were used for the bulk mining of SSR markers and for the construction of the first globe artichoke microsatellite marker database. (researchgate.net)

Area of study: Identification of molecular markers linked to crown rot resistance in tomato. (usda.gov)

MADC2 is an example of a polymerase chain reaction -based (PCR-based) genetic marker that has been shown to produce a 390-bp amplicon that correlates with the expression of male phenotypes . (cannaqa.wiki)

Amplicons were sequenced and sequence data assembled into contigs. (zfin.org)

An overlap of SNPs called by each mapping algorithm determined our set of high confidence SNPs which were subsequently used for phylogenetic and comparative SNP analysis. (sun.ac.za)
18S rRNA was the first genetic marker used for phylogenetic classification of nematodes 4 . (nature.com)

SSRs were screened against 3 mapping populations. (arizona.edu)
Two hundred and sixty-five SSRs were genetically mapped in at least one population. (arizona.edu)
Of the 265 mapped SSRs, 60 came from BAC singletons not yet placed into contigs of the physical map. (arizona.edu)

Centromeric regions were inferred from recombination frequencies of genetic markers, alignment of 303 bp centromeric sequence with the PGA, and heat map showing the physical contact matrix over the entire genome. (oregonstate.edu)
Mitochondrial minicircle contigs were assembled with a kmer list of 99, 109, 119, circularized (removing overlapping contig ends) and polished (reorientation and alignment) using KOMICS v.1.8. (howest.be)

Therefore, the "co-segregation" patterns of all markers can be used to reconstruct their order. (wikipedia.org)

Three mapping algorithms were used to align the Illumina paired-end reads to the M. tuberculosis reference H37Rv. (sun.ac.za)

The physical map of 5DS was comprised of 164 contigs, of which 45 were organized into 21 supercontigs, covering 176 Mb with an N50 value of 2,173 kb. (biomedcentral.com)
Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L. (tamu.edu)
Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic map. (oregonstate.edu)

Maps provide researchers with the opportunity to predict the inheritance patterns of specific traits, which can eventually lead to a better understanding of disease-linked traits. (wikipedia.org)

These unique molecular patterns in the DNA are referred to as polymorphisms, or markers. (wikipedia.org)
Approximately 200-300 cells from samples of both benign liver or HCC from a patient were encapsulated and unique molecular barcoded using a Gel Beads-in emulsion (GEM) system. (elifesciences.org)
The resulting 10x Adapter sequence contains a 16-base pair barcode, followed by a 12-base pair unique molecular identifier (UMI) and a 30-base pair poly(dT) sequence. (elifesciences.org)

Whole genome analysis reveals new insights into the molecular characteristics of Clostridioides difficile NAP1/BI/027/ST1 clinical isolates in the People's Republic of China. (cdc.gov)

Several other CBB resistance QTL have been identified but none of them have been physically mapped. (tamu.edu)
Four molecular markers tightly linked to this QTL have been identified suitable for marker assisted selection and physical mapping of the resistance gene. (tamu.edu)
Molecular characterization of Campylobacter causing human clinical infection using whole-genome sequencing: Virulence, antimicrobial resistance and phylogeny in Ireland. (cdc.gov)
More robust resistance can be obtained by combining NLRs with different recognition specificities ( 15 - 18 ), or by including pattern recognition receptors (PRRs), which recognize conserved (microbe- or pathogen-derived) molecular patterns. (elifesciences.org)

The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples. (bvsalud.org)

There are two distinctive mapping approaches used in the field of genome mapping: genetic maps (also known as linkage maps) and physical maps. (wikipedia.org)

We looked at which parts of the genome in the neurons of the cerebral cortex have active promoters, using a special chromatin marker, and thus scanned the entire genome. (vechnayamolodost.ru)

For these fingerprinted contigs (FPC) a high percentage of the mapped markers showed inconsistent map locations. (arizona.edu)
With these markers developed for high-throughput testing assays, the cannabis industry will be able to easily screen and select for the desired sex of a given cultivar depending on the application. (cannaqa.wiki)
The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome. (oregonstate.edu)
Animal's and microorganisms' secretions, as well as plant extracts, have been used as folk medicine since the dawn of the humanity [ 1 ].Therefore, molecules found in poisons and venoms are interesting, once they were selected by evolution to act in their molecular targets with high specificity [ 1 , 2 ]. (biomedcentral.com)

In 2008, total world production was about 576,000 metric tons with a total export value estimated around 2.4 billions USD ( http://www.fao.org/fishery/statistics/en ). (biomedcentral.com)
A total of 9.110 minicircle contigs were assembled across all strains, of which 78% were successfully circularized. (howest.be)

It's evolution and biological characteristics in Cape Town have been investigated using a variety of molecular markers resulting in the identification of 7 sub-lineages. (sun.ac.za)

Here we report the construction of 12 BAC/BES framework physical maps derived from these libraries and an analysis of the BESs in terms of transposable element, simple sequence repeat (SSR), microRNA (miRNA), and single nucleotide variation (SNV) content. (biomedcentral.com)
Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. (biomedcentral.com)

Use of Whole Genome Sequencing for the Molecular Comparison of Neisseria gonorrhoeae Isolates With Decreased Susceptibility to Extended Spectrum Cephalosporins From 2 Geographically Different Regions in America. (cdc.gov)
it aims to detect the inheritance pattern of a particular disease, localize the gene and find a marker associated with disease susceptibility. (bvsalud.org)

Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. (frontiersin.org)

Molecular tools, in particular, will allow researchers to determine whether changes in gene frequencies provide insight into the effectiveness of treatment, understand the impacts of treatment on the gene pool and population structure of Schistosoma parasites, and establish whether movement of humans from refugia or non-treated areas introduces new parasites into local populations [ 4 ]. (biomedcentral.com)

A new method was developed for separation of partially digested large-molecular-weight DNA fragments that facilitated library construction with large inserts. (johnshopkins.edu)

In some areas of study, gene mapping contributes to the creation of new recombinants within an organism. (wikipedia.org)

Williams 82') has made it important to integrate its physical and genetic maps. (arizona.edu)

The super-contig was searched to identify the sequence adjacent to the IS6110 location. (sun.ac.za)
To reliably demonstrate T.b. gambiense infections, we want to identify a new molecular marker that is fully specific for T.b. gambiense (type I) from diverse geographical origins and that is more sensitive than current genetic markers. (howest.be)

Characterisation of molecular DNA rearrangements within the Xq12-q13.1 region, in three patients with X-linked hypohidrotic ectodermal dysplasia (EDA). (ox.ac.uk)

The genetic basis to gene maps is to provide an outline that can potentially help researchers carry out DNA sequencing. (wikipedia.org)
These genome resources provide the material basis for future microarray development, marker validation, and genetic linkage and QTL analysis. (nih.gov)

Anatomy14

Organisms1

Diseases1

Chemicals and Drugs7

Analytical, Diagnostic and Therapeutic Techniques and Equipment24

Phenomena and Processes43

Disciplines and Occupations2

Anthropology, Education, Sociology and Social Phenomena1

Information Science5

Health Care1

Genes19

Chromosome12

Clones9

Genetics3

Genomic6

OVERGO HYBRIDIZATION1

Biology2

Sequences6

Chromosomes8

Functional annotation1

BACs3

Locus1

Loci3

Epidemiology2

Assembly4

Microsatellite3

Tomato1

Polymerase Chain Re1

Sequence Data1

Phylogenetic2

SSRs3

Alignment2

Reconstruct1

Reads1

Physical map3

Traits1

Unique molecular3

Genome analysis1

RESISTANCE4

Patterns1

Linkage maps1

Entire genome1

High4

Total2

Identification1

Libraries2

Susceptibility2

Species1

Populations1

Construction1

Study1

Genetic maps1

Identify2

Rearrangements1

Basis2