Bacterial artificial chromosome contig mapping. Medical search. Frequent questions

Genomic and cDNA sequence alignments as well as chromosome localization using nullisomic-tetrasomic lines provided strong evidence for three expressed gene copies located on homoeolog chromosomes for TaSK1 as well as for TaSK2 . (biomedcentral.com)

The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. (frontiersin.org)
Distribution and expression of the genes on chromosome 1. (nature.com)
Radiation hybrid maps have a resolution power intermediate to that of the genetic and BAC contig maps and are also a powerful tool for the mapping of ESTs and genes by simple PCR. (biomedcentral.com)
This information was used to develop markers from chicken EST sequence data orthologous to genes in these human regions, in addition to the existing markers from the chicken chromosome 5 genetic map. (biomedcentral.com)
We have contributed to the assembly process by mapping markers/genes to BACs and contigs using overgo hybridization. (kent.ac.uk)
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)
The sequence was used to map 110 ESTs and to predict new genes, including two GenScan gene predictions that overlapped ESTs and were shown to be differentially expressed in tumorigenic and suppressed A549 cell lines. (elsevierpure.com)
Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. (biomedcentral.com)
BAC libraries are essential elements in doing large-scale genome research such as screening for genes of target, biosynthetic gene cluster cloning, transgene identification, gene/gene cluster functional analyses, physical mapping and genome sequencing. (biost.com)
Our results revealed that the FOXP1 and TP63 genes were both relocated along chromosome 3. (biomedcentral.com)
The difference appears to be purely methodological, as Kent and Zahler analyzed a subset of the data of Coghlan and Wolfe, and probably derives from a more relaxed definition of matching genes and use of cosmid fingerprinting physical map information by the latter study [ 6 ]. (biomedcentral.com)
As a scientist she has been involved in mapping the human genome and identifying genes and mutations, which give rise to heritable disorders. (bepress.com)
Preliminary analyses using 454 transcriptome and Bacterial Artificial Chromosome (BAC) sequences from three Heliconius species highlighted a cluster of genes within each region showing relatively higher rates of sequence evolution. (biomedcentral.com)
Introgression of Bacterial Blight Resistance Genes in the Rice Cultivar Ciherang: Response against Xanthomonas oryzae pv. (mdpi.com)

End sequence generated in the construction of the BAC/PAC contig identified a previously unmapped EST and served to order genomic sequence contigs from the publicly available Celera Genomics (CG) and Human Genome Project (HGP) efforts. (elsevierpure.com)
We have tremendous experience with plant, animal, yeast and bacterial genomic BAC libraries. (biost.com)
An important breakthrough in horse Y chromosome research came with the availability of new genomics tools and resources, such as large-insert genomic bacterial artificial chromosome (BAC) libraries (for review, see Rubes et al. (veteriankey.com)
2009), chromosome flow sorting and microdissection technology, and various genomic DNA amplification systems (Telenius et al. (veteriankey.com)
Chromosome localization and genomic structure of the KiSS-1 metastasis suppressor gene (KISS1). (shengsci.com)

Die Analyse großer Cosmid- und BAC- (Bacterial Artificial Chromosome) Contigs, welche im Rahmen dieser Arbeit erstellt wurden und die mehr als 1 Mb sowohl des X- als auch des Y-Chromosoms des Platys X. maculatus abdecken, zeigte eine hohe Dichte von Retroelementen und anderen repetitiven Sequenzen, besonders im Bereich des dominanten Onkogens Xmrk und in einer durch das duplizierte Gen ps-criptY gekennzeichneten, Y-spezifischen Region. (uni-wuerzburg.de)
Although this technology was developed much later than Yeast Artificial Chromosome (YAC) and cosmid/fosmid based genome library cloning technologies it soon became popular and tractable because of the technical advantages offered by BAC based cloning over YAC and cosmid/fosmid library cloning systems:1. (biost.com)

Introduction of a 1.1 Mb fragmented yeast artificial chromosome (YAC) mapping to this region completely suppresses the tumorigenic properties of a human NSCLC cell line, A549. (elsevierpure.com)

The 120 Mb of euchromatin is on two large autosomes and the X chromosome. (harvard.edu)
Compared to autosomes and the X chromosome, relatively few numerical or structural cytogenetic abnormalities have been reported for ECAY. (veteriankey.com)

Here we develop a sequencing-based "in vitro" linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of "subhaploid" fosmid/bacterial-artificial-chromosome clone pools, and by restriction site-associated DNA sequencing of these clone pools to produce an ultradense whole-genome restriction map to facilitate genome scaffolding. (pacb.com)

A major quantitative trait loci (QTL) conditioning common bacterial blight (CBB) resistance in common bean (Phaseolus vulgaris L.) lines HR45 and HR67 was derived from XAN159, a resistant line obtained from an interspecific cross between common bean lines and the tepary bean (P. acutifolius L.) line PI319443. (tamu.edu)

Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. (frontiersin.org)
We present whole-genome profiling (WGP), a novel next-generation sequencing-based physical mapping technology for construction of bacterial artificial chromosome (BAC) contigs of complex genomes, using Arabidopsis thaliana as an example. (ampliconexpress.com)
Comparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. (biomedcentral.com)

Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L. (frontiersin.org)
This sequence-based physical map will be useful to assemble the genome sequence of pea. (frontiersin.org)
In the current study, we have undertaken construction of a sequence-based physical map of pea to address the challenge in the assembly of these repetitive sequences and overcome the shortcomings of traditional restriction digestion based physical maps. (frontiersin.org)
WGP technology is based on generation of short sequence tags from terminal ends of restriction fragments of individual BAC clones, followed by assembly of BAC clones into contigs based on shared regions containing identical sequence tags. (frontiersin.org)
WGP is designed based on the use of sequence tags generated by next generation sequencing (NGS) and is a powerful alternative to traditional DNA fingerprinting based physical mapping technologies, and also simultaneously generates a partial genome sequence. (frontiersin.org)
To confirm the validity of the map and to provide valuable comparative mapping information, both markers from the genetic map and a high number of ESTs (Expressed Sequence Tags) were used. (biomedcentral.com)
Only two discrepancies were observed in relation to the sequence assembly recently reported for this chromosome. (biomedcentral.com)
While in the process of finishing our map, the first draft sequence assembly of the chicken genome was released (March 1st, 2004). (biomedcentral.com)
The quality of both the GGA5 RH map and of the sequence assembly was therefore checked by alignment of all the markers by BLAST searches. (biomedcentral.com)
Abstract: '[Researchers] have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. (harvard.edu)
P. 2194 middle column 2nd paragraph: 'Genome assembly relied on the use of several types of data, including clone-based sequence, whole-genome sequence from libraries with three insert sizes [2 kb, 10 kb, and 130 kb], and a Bacterial Artificial Chromosome (BAC)-based sequence-tagged site (STS) content map. (harvard.edu)
Our strategy is to develop bacterial artificial chromosome (BAC)-end sequence (BES) physical frameworks of the ten genome types of Oryza and align them to the reference sequence. (biomedcentral.com)
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)

Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. (frontiersin.org)
In addition, a 550-kbp contig composed of 6 BAC clones was constructed that encompassed two adjacent RFLP markers on chromosome 2. (johnshopkins.edu)
A bacterial artificial chromosome (BAC) library was constructed from high molecular weight DNA of HR45 and is composed of 33,024 clones. (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)

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)
The probes have been used for molecular hybridizations (fluorescence in situ hybridization, or FISH) in clinical cytogenetics, Y chromosome mapping, sequencing, gene discovery, and comparative Y chromosome studies between the horse and other equids/ Perssodactyls. (veteriankey.com)

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)

Here we report on a 79-year woman with an aggressive form of myelodysplastic syndrome with del(5q), no TP53 mutation, and a novel complex rearrangement of chromosome 3 in bone marrow cells. (biomedcentral.com)
The complex chromosome 3 rearrangement was found in all the metaphases, strongly suggesting its role as a driver mutation. (biomedcentral.com)

These WGP tags were used to assemble 220,013 BACs into contigs. (frontiersin.org)
We've assigned over 6000 BACs to over 600 markers across almost all chicken chromosomes and linkage groups. (kent.ac.uk)

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)

1997 ). Mapping probes: SSR p-umc1022 (Sharopova et al. (wikipedia.org)
1997 ), on chromosome 7, another by igl1, indole-3-glycerol phosphate lyase1(Frey et al. (wikipedia.org)
1997, on chromosome 1, and another by tsah1, 'TSA like" and located near the bx1 gene (Frey et al. (wikipedia.org)

Loss of heterozygosity for a locus on human chromosome 11q22-23 is observed at high frequency in non-small cell lung carcinoma (NSCLC). (elsevierpure.com)
Peach fruit acidity is controlled by a large-effect D locus on chromosome 5. (bvsalud.org)
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)

Vertebrate chromosomes are mosaic structures containing large conserved segments that can reside in different linkage groups in different species. (biomedcentral.com)

Construction and characterization of a bovine bacterial artificial chromosome library. (shengsci.com)

Moreover, once framework RH maps of a genome have been constructed, a quick location of markers by simple PCR on the RH panel is possible. (biomedcentral.com)
The final map is composed of 73 framework markers extending over a 1315.6 cR distance. (biomedcentral.com)
The high resolution framework map obtained in this study has markers covering the entire chicken chromosome 5 and reveals the existence of a high number of rearrangements when compared to the human genome. (biomedcentral.com)
The chicken genetic map is about 4000 cM, with 2000+ molecular markers mapped using three major reference families. (kent.ac.uk)
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)

Single additional alterations to del(5q) by balanced chromosome rearrangements were rarely found in myelodysplasia. (biomedcentral.com)
Conversely, balanced chromosome rearrangements were rarely found as a single additional alteration to del (5q). (biomedcentral.com)
Estimation of rates of intrachromosomal to between-chromosome rearrangements showed that both were very frequent (approximately fourfold greater than that observed in D. melanogaster ). (biomedcentral.com)
This might be because rearrangements in the gene-poor Y chromosome have milder effect on the phenotype, as a result of which the affected individuals escape attention and are not subjected to cytogenetic analysis. (veteriankey.com)
The only true Y chromosome structural rearrangements, reported so far, are large-scale ECAY deletions in 64,XY sex reversal mares (Raudsepp et al. (veteriankey.com)

The combination of these resources resulted in a set of ordered contigs spanning nearly all of the euchromatic region on each chromosome arm. (harvard.edu)
This polymorphism is primarily attributed to the various amount of Y heterochromatin, though earlier studies also suggest variation in the euchromatic portion of the chromosome (Power, 1988). (veteriankey.com)

Both bacterial artificial chromosome (BAC) and small insert sequencing libraries have been constructed from DNA of a single female inbred Red Jungle Fowl, the nearest wild relative of domestic chickens. (kent.ac.uk)

2014) Convergent bacterial microbiotas in the fungal agricultural systems of insects . (doe.gov)

Aneuploidy is an abnormality in the number of chromosomes in a cell due to loss or duplication. (genome.gov)

Overgo (physical map probe) PCO06449 (Gardiner et al. (wikipedia.org)

WGP TM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. (frontiersin.org)
Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L. (tamu.edu)

2014) A taxonomy of bacterial microcompartment loci constructed by a novel scoring method . (doe.gov)

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)

Therefore, microdissected Y-chromosome probes are good for FISH but not suitable for cloning and sequencing of the male-specific or pseudoautosomal regions of the chromosome. (veteriankey.com)

2014) High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly . (doe.gov)

Southern blot analysis of EcoRI-digested mouse cellular DNA with this probe detected four restriction fragments, all of which appear to be located on mouse chromosome 7, Northern blot analysis using the mouse probe demonstrated that related mRNA species were expressed in some normal adult mouse tissues. (shengsci.com)

To further localize the gene(s) responsible for this partial suppression, a bacterial artificial chromosome (BAC) and P1-based artificial chromosome (PAC) contig was constructed, completely spanning the candidate region. (elsevierpure.com)
Partial metaphases showing the normal and the rearranged chromosome 3. (biomedcentral.com)

A bacterial artificial chromosome (BAC) library has been constructed for use in bovine genome mapping using constructed for use in bovine genome mapping using the pBeloBAC11 vector. (shengsci.com)

The available human/chicken comparative mapping data indicated conservation of synteny between GGA5 and portions of HSA11, HSA14 and HSA15. (biomedcentral.com)

Additionally, there are two reports about infertile stallions having XXY sex chromosomes - an equine counterpart to human Kleinfelter syndrome (Kubien et al. (veteriankey.com)

Whole-genome restriction mapping by 'subhaploid'-based RAD sequencing: An efficient and flexible approach for physical mapping and genome scaffolding. (pacb.com)

The chicken ChickRH6 panel recently produced was used here to construct a high resolution RH map of chicken GGA5. (biomedcentral.com)
Finally, this RH map was used for testing the accuracy of the chicken genome assembly for chromosome 5. (biomedcentral.com)

The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. (biomedcentral.com)

Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. (pacb.com)

RadMap outperforms BioNano and Hi-C when input assembly is highly fragmented (contig N50 = 54 kb). (pacb.com)

RadMap can capture wide-range contiguity information and provide an efficient and flexible tool for high-resolution physical mapping and scaffolding of highly fragmented assemblies. (pacb.com)

The main part deals with examples of modern FISH-applications, highlighting unique possibilities of the approach, like the possibility to study individual cells and even individual chromosomes. (frontiersin.org)

The X-ray structure of BX1 protein has been resolved and compared with bacterial TSA (tryptophan synthase alpha subunit, Kulik et al. (wikipedia.org)

The only disadvantage to this type of library is that it cannot be used for physical mapping or full-genome sequencing. (biost.com)

The average contig size is 0.33 Mbp and the N 50 contig size is 0.62 Mbp. (frontiersin.org)
The genome was confirmed to comprise eight chromosomes (chromosomes 1-8 in decreasing size), the assignment of which is different from a previous report 7 ( Supplementary Table S1 and schematic drawing in Supplementary Fig. S1 ). (nature.com)

He suggested to introduce the term chromosomics being equal to cytogenomics to bring the three-dimensional morphologically of chromosomes into the focus of research, as this is essential for gene regulation. (frontiersin.org)

Anatomy38

Organisms10

Diseases7

Chemicals and Drugs7

Analytical, Diagnostic and Therapeutic Techniques and Equipment19

Phenomena and Processes70

Disciplines and Occupations1

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Information Science3

Expressed gene1

Genes15

Genomic5

Cosmid2

Yeast artificial1

Autosomes and the X chromosome2

Fosmid1

Quantitative Trai1

Genomes3

Sequence13

Clones5

Hybridization2

Analyses1

Rearrangement2

BACs2

Fingerprint1

19973

Locus3

Vertebrate1

Characterization1

Markers5

Rearrangements5

Euchromatic2

Libraries1

Fungal1

Abnormality1

Overgo1

Physical map2

Loci1

Positional1

Probes1

Eucalyptus1

Species1

Partial2

Bovine1

Comparative1

Human1

Whole genome1

Chicken2

Consists1

Linkage maps1

Assembly1

High1

Study1

Protein1

Library1

Size2

Research1