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2 edition of Construction of a cosmid contig on chromosome 12 found in the catalog.

Construction of a cosmid contig on chromosome 12

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Published .
Written in English


Edition Notes

Statementby Cassandra Thomas
The Physical Object
Pagination69 leaves :
Number of Pages69
ID Numbers
Open LibraryOL24400703M

  Our goal is to construct a robust physical map for maize (Zea mays) comprehensively integrated with the genetic map. We have used a two-dimensional 24 × 24 overgo pooling strategy to anchor maize expressed sequence tagged (EST) unigenes to , bacterial artificial chromosomes (BACs) on high-density filters. A set of 70, public maize ESTs seeded derivation of 10, EST Cited by: Physical Mapping and Sequencing of Human Chromosome l6p Mb cosmid!P1 contig of the human chromosome region in 16p extending from the tnberous sclerosis disease (TSC2) locus to the CREB binding Human Genome Program, of the U.S. Department of Energy under Contract -ACSF This is the 12 page Bundled Homework package with Answer Key that chronologically follows and my six part now 3, slide DNA and Genetics Unit that I offer on TpT. Other topics in the homework bundle are cell division (mitosis and meiosis), Cancer, Skin Cancer, Anti-tobacco, and Bioethics. The remaining chapters present protocols for the construction of various types of clone libraries and for the assembly of contig maps. Chapter 7 describes the construction of cosmid libraries from bacterial DNA and the construction of contig maps by comparing restriction maps and by chromosome walking.


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Construction of a cosmid contig on chromosome 12 by Cassandra Thomas Download PDF EPUB FB2

Contig Mapping. Strategy. A physical map is the ordering of cosmid clones by their position along a chromosome. Construction of a physical map begins with the creation of an initial, partially ordered collection of clones, which is then edited to create a final map.

Physical contig mapping. The relevant cosmid is digested with a restriction enzymes pannel (4–5 enzymes, 5 µg cosmid per digest) in order to produce cosmid fragments spread between 12 and kb. The appropriate digests (at least four) are then individually loaded into the wells of 1% agarose minigels, electrophoresed under standard.

As a prerequisite for positional cloning of the DFN3 gene, a kb cosmid contig spanning the critical region was constructed by subcloning of two YACs and by cosmid walking in the ICRF X-chromosome library.

Using Southern- and PFGE-analysis, we were able to identify 2 novel microdeletions and a kb duplication associated withmore». A yeast artificial chromosome (YAC), P1, and cosmid clone contig was constructed for the Werner syndrome (WRN) region of chromosome 8pp21 and used to clone a candidate gene for WRN.

This region also possibly contains a familial breast cancer locus. The Gossypium hirsutum homoeologous chromosome 12 encodes important genes that contribute to fiber fuzz, lethality, gland development and male sterility.

In this study a physical map of the cotton TM-1 chromosome 12 was constructed. A number of large-insert cotton genome libraries are available, and genome-wide physical mapping using large insert segments combined with bacterial Author: Yanhui Lv, Dan Ma, Wenhua Liang, Yuanda Lv, Wangzhen Guo, Yan Hu, Tianzhen Zhang.

Cosmid vectors are plasmids that contain a small region of bacteriophage λ DNA called the cos sequence. This sequence allows the cosmid to be packaged into bacteriophage λ particles. GENOM () Evaluation of a Cosmid Contig Physical Map of Human Chromosome 16 RAYMOND L.

STALLINGS,* NORMAN A. DOGGETT,* DAVID CALLEN,t SINOULA APOSTOLOU,t L. ZHONG CHEN,t JULIE K. NANCARROW,t SCOTT A. WHITMORE,t PETER HARRIS, HANNAH MICHISON,MARTIJN BREUNING,I1 JASPER J. SARIS," JAMES FICKETT,** MICHAEL Cited by:   RESULTS: All available markers on chromosomes A12 and D12 were used to screen the TM-1 BAC library by PCR.

A total of clones ( for A12, for D12) were obtained using Hind III fingerprinting and used for construction of the contig map. Seven pairs of SSR markers located on A12 and D12 were chosen for contig : Yanhui Lv, Dan Ma, Wenhua Liang, Yuanda Lv, Wangzhen Guo, Yan Hu, Tianzhen Zhang.

A cosmid contig physical map of human chromosome 16 has been developed by repetitive sequence finger-printing of ∼ cosmid clones obtained from a chromosome specific cosmid library. The arrangement of clones in contigs is determined by (1) estimating cosmid length and determining the likelihoods for all possible pairwise clone overlaps Cited by: A contig (from contiguous) is a set of overlapping DNA segments that together represent a consensus region of DNA.

In bottom-up sequencing projects, a contig refers to overlapping sequence data (reads); in top-down sequencing projects, contig refers to the overlapping clones that form a physical map of the genome that is used to guide sequencing and assembly. Construction of BAC contig maps of homoeologous chromosomes A12 and D12 of Gossypium hirsutum L.

acc. TM-1 Yanhui Lv, Dan Ma, Wenhua Liang, Yuanda Lv, Wangzhen Guo, Yan Hu* and Tianzhen Zhang* Abstract Background: The Gossypium hirsutum homoeologous chromosome 12 encodes important genes that contribute to.

Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencing technologies have favored lowering per-base cost at the expense of read length.

This has dramatically reduced sequencing cost, but resulted in fragmented assemblies, which negatively affect downstream analyses and hinder the creation of finished (gapless, high-quality. Chromosomes are inherited as intact units, so it was reasoned that the alleles of some pairs of genes will be inherited together because they are on the same chromosome (Figure ).

This is the principle of genetic linkage, and it was quickly shown to be correct, although the. The CEA-like gene family was determined by fluorescence in situ hybridization to map in the qq region of human chromosome Analysis of the two CEA-subgroup contigs provided verification of the contig assembly strategy and insight into the organization of 9 CEA-subgroup by: The development of P1-artificial chromosome (PAC) 12 and bacterial artificial chromosome (BAC) 13 cloning systems was pivotal to the success of the whole-genome map.

They provided larger inserts Author: John D. Mcpherson. We have constructed and characterized two related human chromosome specific cosmid libraries. DNA from flow-sorted chromosomes from a somatic cell hybrid was cloned into a cosmid vector. A contig is a chromosome map showing the locations of those regions of a chromosome where contiguous DNA segments overlap.

Contig maps are important because they provide the ability to study a complete, and often large, segment of the genome by examining a series of overlapping clones which then provide an unbroken succession of information. Fine-mapping and construction of a bovine contig spanning the ovine callipyge locus Article (PDF Available) in Mammalian Genome 12(2) February with 43 Reads How we measure 'reads'.

Probe c hybridizes to the region of 3q that remains with chromosome 3 and probes a, b, and d hybridize to the region of 3q that is translocated in this case to chromosome b.

Because translocations of chromosome 3 that break band 3q are correlated to the disease, it is reasonable to assume that these rearrangements split the normal. Analysis of chromosome construction of STS map and its application for contig map construction.

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, 38 (3), Author: Y. Sakaki, M. Hattori, H. Tanahashi, Takashi Ito, Kosuke Tashiro. Abstract. We have applied a yeast artificial chromosome (YAC)-based cosmid isolation and binning strategy to convert a YAC contig in Xp22 into Mb of overlapping cosmids.

This strategy is based on the screening of a high-density arrayed X chromosome-specific cosmid library with large YAC-derived restriction fragments and entire YAC by: Ensembl ENSG ENSMUSG UniProt Q Q RefSeq (mRNA) NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ RefSeq (protein) NP_ NP_ NP_ NP_ NP_ NP_ n/a Aliases: SEMA3B, LUCA-1, SEMA5, SEMAA, SemA.

Chromosome Contigs Clones Construction of YACs and BACs High-Molecular Weight DNA Partial Restriction Digestion Si ze Se l S i z e S ction c t o n YAC Vector Arms BAC Vector Ligate & Transform into Yeast Ligate & Transform into Bacteria YAC Insert: ~ kb BAC Insert: ~ kb Telomeres Yeast DNA Plasmid DNA Insert DNA BAC Vector.

A quick look I can see that the value you gave to -genome is wrong. It should be only hg19 in your case. Just type./cnvnator and you will see something like this at the end. Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19, mm9. The obvious one is using more sequence data, either paired-end (short inserts) or mate-pair 2nd gen reads (longer distances), or fosmid/cosmid/BAC ends (typically sequenced using Sanger).

I'm using RNAseq for this, which seems an obvious thing to do, but I'm not sure it's very common. You can use a related genome, and map your contigs to that. In genome assembly, scaffolds are organized from contigs using discontinuous sequence information which provides incomplete information as to the distance between contigs and may not even orient them relative to each other.

There are several commo. Ultra-long contigs provide complete and uninterrupted sequence information across full genes, and more recently even allow separation of the two chromosomes for diploid organisms.

1 The unprecedented quality of PacBio de novo genome assemblies has been described in many publications, such as the gorilla genome assembly with a contig N50 of   A BAC library was constructed from the genomic DNA of an intergeneric Citrus and Poncirus hybrid.

The library consists of 24, clones with an average insert size of kb, representing approximately seven haploid genome equivalents and is able to give a greater than 99% probability of isolating single-copy citrus DNA sequences from this by: A bacterial artificial chromosome (BAC) is a DNA construct, based on a functional fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E.

coli. F-plasmids play a crucial role because they contain partition genes that promote the even distribution of. bacterial artificial chromosome (BAC) vectors originally constructed from the F plasmid - a special plasmid that controls mating and the transfer of genetic material in some bacteria; see Chapter 6) and can hold very large fragments of DNA that can be as long asbp.

Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

Construction, Complete Sequence, and Annotation of a BAC Contig Covering the Silkworm Chorion Locus Zhiwei Chen Junko Nohata See next page for additional authors Creative Commons License Creative Commons License This work is licensed under aCreative Commons Attribution License. 3 Figure 2: Approximate predicted location of contig14 in chromosome 4, using the model for D.

melanogaster shown in Ensembl. Genes Contig CG (3 isoforms) Contig CGContig SoxF (2 isoforms) A. Initial Predictions Upon receiving the contig, the first step that was taken was the perusal of all the previous. contig (kən′tig) (genetics) A region of chromosome defined by its hybridization to one or more cloned deoxyribonucleic acid fragments from an Full article >>> A contig is a set of gel readings that are related to one another by overlap of their sequences.

The ovine Major Histocompatibility Complex (MHC) harbors genes involved in overall resistance/susceptibility of the host to infectious diseases. Compared to human and mouse, the ovine MHC is interrupted by a large piece of autosome insertion via a hypothetical chromosome inversion that constitutes ~25% of ovine chromosome The evolutionary consequence of such an inversion and Cited by: 6.

The finished sequence of human chromosome 20 compri, base pairs (bp) and represents % of the euchromatic DNA.

A single contig of. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome.

Here we present the finished sequence of human chromos which has been finished to high quality and spans approximately megabases, representing approximately % of.

Construction of genomic library using yeast artificial chromosome are linear DNA molecules containing the necessary features of an authentic yeast.

Start studying Genetics Chap Learn vocabulary, terms, and more with flashcards, games, and other study tools. Search. Genes on a chromosome are arranged in a linear array, and the physical distance between them dictates the frequency of crossing over between them. cosmid. a hybrid between a plasmid vector and phage lambda.

Rf1 is a nuclear gene that controls fertility restoration in cases of cytoplasmic male sterility caused by the Owen cytoplasm in sugar beet. In order to isolate the gene by positional cloning, a BAC library was constructed from a restorer line, NK, with the genotype Rf1Rf1.

The library contai clones with an average insert size of kb, providing genome by:. Genome assembly is typically a two-stage process: contig assembly followed by the use of paired sequencing reads to join contigs into scaffolds.

Scaffolds are usually the focus of reported assembly statistics; longer scaffolds greatly facilitate the use of genome sequences in downstream analyses, and it is appealing to present larger numbers as metrics of assembly performance.GeneStudio's Contig editor includes a contig assembly function.

To assemble contigs. Import the sequences you wish to assemble. Press the Assemble button on the toolbar. This will cause the Trim ends dialog to be displayed. Review the trimming options, then press OK to start the assembly.I used software MUMmer to get alignment of the scaffolds to the reference chromosome.

Now I have scaffolds and their respective coordinates on the reference chromosome. I would like to know if there is a software/tool to assemble these scaffolds to chromosome.