A contig of 36 overlapping yeast artificial chromosome (YAC) clones has been constructed for the complete Duchenne muscular dystrophy (DMD) gene in Xp21. The YACs were isolated from a human 48,XXXX YAC library using the DMD cDNA and brain promoter fragments as hybridization probes. The YAC clones were characterized for exon content using HindIII or EcoRI digests, hybridization of individual DMD cDNA probes, and polymerase chain reaction (PCR) amplification of specific exons near the 5 end of the gene. For comparison to the known long-range restriction map of the DMD gene, YAC clones were digested with SfiI and hybridized with DMD cDNA probes. The combined analysis of the exon content and the SfiI map allowed an approximately 3.2-Mb YAC contig to be constructed. The complete 2.4-Mb DMD gene could be represented in a minimum set of 7 overlapping YAC clones.
To test whether human GATA-1 (hGATA-1) is involved in the transcriptional control of globin gene switching, transgenic mice were produced overexpressing hGATA-1. These were crossed with mice carrying a human beta-globin locus yeast artificial chromosome (beta YAC), and globin gene expression was analyzed in their progeny. Mice carrying both the hGATA-1 and the beta YAC transgenes have normal levels of gamma- and beta-globin mRNA, with no distortion in the rate or in the timing of gamma-to-beta switch, indicating that hGATA-1 is not involved in the developmental control of gamma- and beta-globin genes. In contrast, mice carrying the hGATA-1 and the beta YAC transgenes have 5- to 6-fold lower expression of the human epsilon globin gene compared with beta YAC mice lacking the hGATA-1 transgene. These results provide direct in vivo evidence that hGATA-1 is a specific repressor of human epsilon gene expression. These findings also suggest that binary transgenic mouse systems based on overexpression ...
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The majority of chromosomal translocations breakpoints are within regions of the genome where few DNA probes are available. The use of yeast artificial chromosomes (YACs) containing long stretches of human DNA allows dispersed DNA markers to be used to identify the position of breakpoints but does not readily allow subcloning of the precise breakpoint within the YAC DNA nor the cDNAs containing the affected genes. We describe a procedure allowing rapid isolation of cDNAs corresponding to genes within a YAC clone. Random cDNA is hybridised to PCR-generated biotinylated fragments of total DNA from a yeast strain harbouring a YAC clone. The hybrids can be recovered to facilitate subsequent cloning of the cDNA molecules. The application of this method to the cloning of cDNA molecules carrying sequences involved in the translocation t(4;11)(q21;q23) is illustrated.
Yeast artificial chromosomes (YACs) are genetically engineered chromosomes derived from the DNA of the yeast, Saccharomyces cerevisiae, which is then ligated into a bacterial plasmid. By inserting large fragments of DNA, from 100-1000 kb, the inserted sequences can be cloned and physically mapped using a process called chromosome walking. This is the process that was initially used for the Human Genome Project, however due to stability issues, YACs were abandoned for the use of Bacterial artificial chromosomes (BAC). Beginning with the initial research of the Rankin et al., Strul et al., and Hsaio et al., the inherently fragile chromosome was stabilized by discovering the necessary autonomously replicating sequence (ARS); a refined YAC utilizing this data was described in 1983 by Murray et al. The primary components of a YAC are the ARS, centromere, and telomeres from S. cerevisiae. Additionally, selectable marker genes, such as antibiotic resistance and a visible marker, are utilized to select ...
From: Dr. Kenneth Fischbeck To: chromosome-22 at net.bio.net.in Subject: chr 22 YAC screening As part of the genome center here in Philadelphia, we have been identifying YACs with chromosome 22 STSs. We screen both a YAC library made locally from 22-only hybrid cell line KG1 and total genomic YAC libraries made by CEPH & Genethon. We now would like to make this service available to the genetics community in general. For anyone who submits primers for a chromosome 22 STS, we will screen the YAC libraries with the STS and send the positive colonies back to the submitter. There will be no charge for this service. If you are interested in participating, please let me know. K. Fischbeck e-mail: fischbeck at a1.mscf.upenn.edu ...
Originated from a bacterial plasmid, a YAC contains a yeast centromeric region (CEN), a yeast origin of DNA replication, a cluster of unique rectriction sites and a selectable marker and a telomere region at the en of each arm. YACs are capable of cloning extremely large segments of DNA (over 1 megabase long) into a host cell, where the DNA is propagated along with the other chromosomes of the yeast cell.. ...
A vector (abbreviated YAC) used to clone DNA fragments (up to 400 kilobase|kb); it is constructed from the telomere|telomeric, centromere|centromeric, a...
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The large regions of DNA that can be cloned in yeast artificial chromosomes (YACs) are ideal for expression studies of the complex genes and gene clusters found in the mammalian genome. Such studies...
BACKGROUND:Mutagenesis of yeast artificial chromosomes (YACs) often requires analysis of large numbers of yeast clones to obtain correctly targeted mutants. Conventional ways to isolate yeast genomic DNA utilize either ...
Bell CJ, Budarf ML, Nieuwenhuijsen BW, Barnoski BL, Buetow KH, Campbell K, Colbert AM, Collins J, Daly M, Desjardins PR, et al, Integration of physical, breakpoint and genetic maps of chromosome 22. Localization of 587 yeast artificial chromosomes with 238 mapped markers. Hum Mol Genet4:59-69 ...
We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted watermarks at intergenic sites known to tolerate transposon insertions. Overlapping cassettes of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb (1/8 genome), and 144 kb (1/4 genome), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then ...
During the construction of yeast artificial chromosome (YAC) libraries to facilitate mapping of the human genome, two YACs may be cotransformed into the same yeast cell, making further analysis very difficult. We present a simple method to rescue the required YAC that utilizes the segregation of chromosomes at meiosis. In brief, we crossed the cotransformed yeast cell with a non-YAC-containing strain and induced the resulting diploid to sporulate and undergo meiosis. The new haploid generation included some yeast cells that contained only the desired YAC. These YACs were analyzed by conventional methods. To exclude the possibility that major rearrangement occurred during the procedure, we analyzed the YACs with restriction enzymes that cut only rarely. We conclude that this is a useful technique to rescue cotransformed YACs.
A continuous array of overlapping clones covering the entire human chromosome 21q was constructed from human yeast artificial chromosome libraries using sequence-tagged sites as landmarks specifically detected by polymerase chain reaction. The yeast artificial chromosome contiguous unit starts with pericentromeric and ends with subtelomeric loci of 21q. The resulting order of sequence-tagged sites is consistent with other physical and genetic mapping data. This set of overlapping clones will promote our knowledge of the structure of this chromosome and the function of its genes.
Typically the chromosome also contains a selection marker such as TRP1, Lys2 or Ura3. Minimal size for a YAC is between 50kb and 100kb, while maximum sizes are 1Mb to 3Mb. A common tool for constructing YACs is a shuttle plasmid such as pYAC4 which replicates in E. coli, has a multiple cloning site, and a pair of telomeres which can be cleaved to form a linear fragment. Available as an E.coli plasmid ATCC 67379, sequence at U01086. There are two common centromere sequences, CEN4 and CEN6. CEN4 is found in most yeast centromere-containiing vectors, such as pYAC4. These vectors typically use ARS1 sequences. The pRS313- pRS316 plasmids use the CEN6 + ARSH4 cassette (Sikorski89). ...
Herpesvirus of turkey (HVT) is an alphaherpesvirus that is widely used as a live vaccine against Marek's disease because of its antigenic relationship with Marek's disease virus (MDV). In spite of a similar genome structure, HVT has several unique genes, the functions of which are not completely understood. As a first step in carrying out detailed analysis of the functions of the HVT genes, a full-length infectious bacterial artificial chromosome (BAC) clone of HVT was constructed. DNA from two independent BAC clones, upon transfection into chicken embryo fibroblasts, produced plaques similar to those produced by the wild-type virus. Viruses derived from the BAC clones were stable during in vitro passage, but showed differences in in vitro growth kinetics compared with the wild-type virus. Using a one-step mutagenesis protocol to delete the essential glycoprotein B gene from the HVT genome, followed by construction of the revertant virus, BAC clones of HVT were shown to be amenable to standard
Reverse genetics has been an indispensable tool revolutionising insights into viral pathogenesis and vaccine development. Large RNA virus genomes, such as from Coronaviruses, are cumbersome to clone and manipulate in E. coli due to size and occasional instability1-3. Therefore, an alternative rapid and robust reverse genetics platform for RNA viruses would benefit the research community. Here we show the full functionality of a yeast-based synthetic genomics platform to genetically reconstruct diverse RNA viruses, including members of the Coronaviridae, Flaviviridae and Paramyxoviridae families. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples, or synthetic DNA, and reassembled in one step in Saccharomyces cerevisiae using transformation associated recombination (TAR) cloning to maintain the genome as a yeast artificial chromosome (YAC). T7-RNA polymerase has been used to generate infectious RNA to rescue viable virus. Based on this platform we have been
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Subject: Nomenclature and Tact. Gentlesophs,. Please remain aware that here at the Nepenene Somatic Clinic a majority of our clients are from out of town, including many from polities where enhancement is not, as it is in Imperial space, thoroughly pervasive; baselines are not rare to the point of nonexistence; and, indeed, the use of biotechnology is considered with varying degrees of caution, skepticism, and even aversion.. As such, when explaining the function of artificial chromosomes and the fertility-preserving function of the acc3BE complex to our clients, be sure always to refer to its operation by its proper technical name, baselining excision, and not, whatever the current chic snark may be at other augmenteries, as bestiality enable.. A certain junior attendings slip of the tongue has already required me to calm down and make contractual concessions to one offended client this month, and I do not care to do so again.. Am I clear?. Doctor AGATTACCATTAGGCG, EFGc, IRCGE, IFNS ...
The set of clone ends is dumped as part of the gff files: http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/GFF_files.shtml This is the source for the extents displayed in WormBase. The caveat with this is that the true end is not marked up for all clones. The early cosmids do not have such annotations because nobody thought about marking them up. Later cosmids do have clone left and right ends as this became part of the standard procedure. Finally, many of the YACs do not have clone ends because the segment submitted to GenBank/EMBL is much smaller than the full clone, and hence the true ends lie within sequences already finished at that stage of the sequencing (i.e. we never went back to update clone ends in sequence already finished ...
The set of clone ends is dumped as part of the gff files: http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/GFF_files.shtml This is the source for the extents displayed in WormBase. The caveat with this is that the true end is not marked up for all clones. The early cosmids do not have such annotations because nobody thought about marking them up. Later cosmids do have clone left and right ends as this became part of the standard procedure. Finally, many of the YACs do not have clone ends because the segment submitted to GenBank/EMBL is much smaller than the full clone, and hence the true ends lie within sequences already finished at that stage of the sequencing (i.e. we never went back to update clone ends in sequence already finished ...
TY - JOUR. T1 - Construction and characterization of a yeast artificial chromosome library containing 1.5 equivalents of human chromosome 21. AU - Potier, M. C.. AU - Kuo, W. L.. AU - Dutriaux, A.. AU - Gray, J.. AU - Goedert, M.. PY - 1992/10. Y1 - 1992/10. N2 - A library of yeast artificaial chromosomes (YACs) was constructed from a human/hamster somatic cell hybrid containing human chromosome 21 (q11-qter). Cells were embedded in agarose, and the DNA was partially digested with EcoRI, released into solution by agarase treatment of the agarose plugs, ligated into pYAC4, and transferred into yeast. Doule screening of the yeast transformants with human and hamster genomic DNA allowed the selection of clones hybridizing only with human DNA. The library consists of 321 clones, amounting to 1.5 equivalents (61 Mb) of chromosome 21. The mean YAC size calculated from 178 clones is 190 ± 100 kb. Screening of the library with eight sequence-tagged sites gave six positives. Among 21 YACs tested by in ...
Huntingtons disease (HD) is an autosomal dominant neurodegenerative disorder that affects men and women in equal numbers, but some epidemiological studies indicate there may be sex differences in disease progression. One of the early symptoms of HD is disruptions in the circadian timing system, but it is currently unknown whether sex is a factor in these alterations. Since sex differences in HD could provide important insights to understand cellular and molecular mechanism(s) and designing early intervention strategies, we used the bacterial artificial chromosome transgenic mouse model of HD (BACHD) to examine whether sex differences in circadian behavioral rhythms are detectable in an animal model of the disease. Similar to BACHD males, BACHD females display circadian disruptions at both 3 and 6 months of age; however, deficits to BACHD female mouse activity levels, rhythm precision, and behavioral fragmentation are either delayed or less severe relative to males. These sex differences are associated
We have used a 1-Mb YAC containing alpha satellite DNA to construct a functional HAC vector by modification with a selectable marker, human telomeres, and a putative origin of replication. YAC 674E2 was selected for this purpose because of its size from among several YACs identified during screening of a randomly chosen subset of the CEPH YAC library with a degenerate alpha satellite probe. Other than the presence of alpha satellite DNA (14) there was no a priori reason to expect that 674E2 would generate a functional HAC. It is now apparent that L2H2 efficiently forms artificial chromosomes as indicated by the formation of HACs in ≈30% of the clonal cell lines that contained both arms of the HAC vector. Detailed analysis of one of these clonal lines, 64b5, indicates that the HAC formed by L2H2 contains human telomeres, binds CENP-E, and is mitotically stable in the absence of G418 selection for more than 100 generations.. L2H2 DNA did not always form HACs after transfection; it was sometimes ...
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the ...
...Maren Bell and Robert Mortimer Human Genome Center Divisionof Cel... Introduction Transformation of ye... Materials and Methods The YAC use...,Electroporation,of,Yeast,Artificial,Chromosomes,biological,advanced biology technology,biology laboratory technology,biology device technology,latest biology technology
Now that weve learned a bit about F factors, you might imagine how a cloning vector could be created that was based on an F factor origin of replication. We call such engineered F plasmids BACs or Bacterial Artificial Chromosomes. BACs are capable of carrying approximately 200 kbp of inserted DNA sequence, and the F factor origin of replication maintains their level at approximately one copy per cell. Of course, we neednt stop there! We can also use YACs which are Yeast Artificial Chromosomes, and depend on being able to replicate and be maintained in Saccharomyces cerevisiae. YACs can carry approximately 500 kbp of foreign DNA, though they are often criticized due to the problem of natural recombination in the host.. Handling DNA of this size is a real problem, as I have mentioned before, due to the potential for shearing. The way this is solved is to embed the cells from which a library is going to be made, in low melting point agarose. The cells can be lysed in the agarose, simply be ...
In addition to XLacZ+/- mosaics, the suitability of transgenic mice from lines Y001deltaDRR and Y223 [30] (both displaying mosaic corneal GFP expression) were evaluated for wound healing studies. These animals carry a yeast artificial chromosome (YAC) containing the human PAX6 locus [31] into which a GFP reporter gene has been inserted at the PAX6 ATG start codon, placing it under the control of the PAX6 regulatory elements. This also eliminates production of PAX6 protein from the YAC ensuring that wild type Pax6 levels in these mice are unaffected. Both lines demonstrated patterns of GFP-positive and GFP-negative radial corneal stripes (Fig. 5) qualitatively similar to those observed in XLacZ+/- mosaics (Fig. 2). The reason for the mosaic transgene expression is not clear but it probably involves stochastic transgene inactivation early in development so that only a proportion of adult limbal stem cells express GFP. Line Y001 contains a single copy of the YAC with a 10-20 kb truncation, while ...
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SCORE============================================Contig004682============================================ 660 ============================================Contig013845============================================1162 57 --------------------------------------------------------------------------------,JMFF051H21 ,----------------------------------------rJMFF051H21 68 -----------------------------------------------------------------------------------------------,JMFF044I04 ,----------------------------------------------------rJMFF044I04 72 ---------------------------------------------------------------------,JMFF037P06 ,-----------------------------------------------------------------rJMFF037P06 81 ------------------------------------------------------------------------------------------,JMFF025B05 ,-----------------------------------------------------------------rJMFF025B05 110 -----------------------------------------------------------------------------,JMFF028E21 ...
© 2008 Cottingham et al. The production, manipulation and rescue of a bacterial artificial chromosome clone of Vaccinia virus (VAC-BAC) in order to expedite construction of expression vectors and mutagenesis of the genome has been described (Domi & Moss, 2002, PNAS 99 12415-20). The genomic BAC clone was rescued back to infectious virus using a Fowlpox virus helper to supply transcriptional machinery. We apply here a similar approach to the attenuated strain Modified Vaccinia virus Ankara (MVA), now widely used as a safe non-replicating recombinant vaccine vector in mammals, including humans. Four apparently full-length, rescuable clones were obtained, which had indistinguishable immunogenicity in mice. One clone was shotgun sequenced and found to be identical to the parent. We employed GalK recombination-mediated genetic engineering (recombineering) of MVA-BAC to delete five selected viral genes. Deletion of C12L, A44L, A46R or B7R did not significantly affect CD8+ T cell immunogenicity in BALB/c
Expression patterns in the globin gene cluster are subject to developmental regulation in vivo. While the γA and γG genes are expressed in fetal liver, both are silenced in adult erythrocytes. In order to decipher the role of DNA methylation in this process, we generated a YAC transgenic mouse system that allowed us to control γA methylation during development. DNA methylation causes a 20-fold repression of γA both in non-erythroid and adult erythroid cells. In erythroid cells this modification works as a dominant mechanism to repress γ gene expression, probably through changes in histone acetylation that prevent the binding of erythroid transcription factors to the promoter. These studies demonstrate that DNA methylation serves as an elegant in vivo fine-tuning device for selecting appropriate genes in the globin locus. In addition, our findings provide a mechanism for understanding the high levels of γ-globin transcription seen in patients with Hereditary Persistence of Fetal Hemoglobin, and
Fungi are prolific producers of secondary metabolites (SMs) and have been producing 45% of bioactive molecules from all microbial sources since the turn of the century (Bérdy, 2012). Conservative estimates suggest that there are more than 5 million fungal species (Blackwell, 2011), of which fewer than 5% have been described and less than 1% are available in the worlds culture collections (Colwell, 1997). In addition, each of these fungal genomes may harbor 50 or more different SM gene clusters (Norberg et al., 2013). Fungal secondary metabolite (SM) gene cluster sequences available for characterization far outstrip our current ability to characterize each cluster, as most of the fungi are not genetically amendable. To address this post-genomic SM characterization gridlock, we have demonstrated a new technology that generates unbiased shuttle bacterial artificial chromosome (BAC) or fungal artificial chromosome (FAC) libraries, pooled FAC next-gen sequences to rapidly capture all the SM gene ...
Thermal asymmetric interlaced (TAIL-) PCR is an efficient technique for amplifying insert ends from yeast artificial chromosome (YAC) and P1 clones. Highly specific amplification is achieved without resort to complex manipulations before or after PCR. The adaptation of this method for recovery and m …
A P1-derived artificial chromosome is a DNA construct that was derived from the DNA of P1 bacteriophage. It can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. P1 was developed as a cloning vector by Nat Sternberg and colleagues in the 1990s.[1][2] ...
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Schäfer BW، Wicki R، Engelkamp D، Mattei MG، Heizmann CW (1995). Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21: rationale for a new nomenclature of the S100 calcium-binding protein family. Genomics. 25 (3): 638-43. PMID 7759097. doi:10.1016/0888-7543(95)80005-7. ...
Winther, K. T., Thygesen, K. S., Jacobsen, K. W., Schiøtz, J., García de Abajo, F. J. & Puska, M. J.. 01/09/2011 → 13/08/2015 ...
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Molecular genetic studies of the human malaria parasite Plasmodium falciparum have been hampered in part due to difficulties in stably cloning and propagating parasite genomic DNA in bacteria. This is thought to be a result of the unusual A+T bias (|80%) in the parasites DNA. Pulsed-field gel electrophoretic separation of P. falciparum chromosomes has shown that large chromosomal polymorphisms, resulting from the deletion of DNA from chromosome ends, frequently occur. Understanding the biological implications of this chromosomal polymorphism will require the analysis of large regions of genomic, and in particular telomeric, DNA. To overcome the limitations of cloning parasite DNA in bacteria, we have cloned genomic DNA from the P. falciparum strain FCR3 in yeast as artificial chromosomes. A pYAC4 library with an average insert size of approximately 100 kb was established and found to have a three to fourfold redundancy for single-copy genes. Unlike bacterial hosts, yeast stably maintain and propagate
In order to define a functional human centromere sequence, an artificial chromosome was constructed as a reproducible DNA molecule. Mammalian telomere repeats and a selectable marker were introduced into yeast artificial chromosomes (YACs) containing alphoid DNA from the centromere region of human c …
Here we report a technique of laser chromosome welding that uses a violet pulse laser micro-beam for welding. The technique can integrate any size of a desired chromosome fragment into recipient chromosomes by combining with other techniques of laser chromosome manipulation such as chromosome cutting, moving, and stretching. We demonstrated that our method could perform chromosomal modifications with high precision, speed and ease of use in the absence of restriction enzymes, DNA ligases and DNA polymerases. Unlike the conventional methods such as de novo artificial chromosome synthesis, our method has no limitation on the size of the inserted chromosome fragment. The inserted DNA size can be precisely defined and the processed chromosome can retain its intrinsic structure and integrity. Therefore, our technique provides a high quality alternative approach to directed genetic recombination, and can be used for chromosomal repair, removal of defects and artificial chromosome creation. The ...
Department of Genetics, Harvard Medical School, Boston, MA, USA.. A method for construction of bacterial artificial chromosome (BAC) contigs from a yeast artificial chromosome (YAC) physical map is described. An approximately 2 Mb contig, consisting of two large BAC contigs linked by a small YAC, has been assembled in the region around 80 cM of Arabidopsis thaliana chromosome 2. Clones from this contig will facilitate gene isolation in the region and can be used directly as substrates for DNA sequencing.. MeSH Terms ...
A series of 130 DNA probes, hybridized to the CIC YAC library, are ordered along the abscissa. A subset of 58 of the probes, mapped to chromosome 2 by RFLP analysis, serve as contact points between the genetic and physical maps. The positions of markers mapped to the recombinant inbred lines (7) are indicated in cM above the marker names. When a set of probes hybridized to the same YACs, their order is listed by their position in the genetic map (7). If no genetic or auxilliary data (e.g. cosmid contig (4)) was available, the exact probe order is indeterminate and is arbitrarily assigned.. A line drawn above a marker indicates a difference in marker order between the physical and genetic maps. Markers designated RI have been mapped by us to the recombinant inbred populations and are in correct relative position (with one exception, 15414, marked RI-?) to the markers on either side (no number is indicated as adding markers and using a different mapping program generates different absolute ...
Medical definition of bacterial artificial chromosome: a genetically engineered bacterial chromosome that is used as a vector to clone DNA segments, …
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