He contributed to the first physical map of the Human Genome at Genethon and at Genset Corporation as a member of Daniel Cohen [fr]'s team, collaborating with research teams from Caltech and the Los Alamos National Lab. (wikipedia.org)
Adjacent gene pairs in the yeast genome have a tendency to express concurrently. (biomedcentral.com)
Our findings suggested that the commonly shared cis -regulatory system does not solely contribute to the co-expression of adjacent gene pairs in yeast genome. (biomedcentral.com)
In a case study, the function for Xenopus laevis contig sequences was predicted and the results are publicly available at ftp://genome.dkfz-heidelberg.de/pub/agd/gene_association.agd_Xenopus . (biomedcentral.com)
OpGen's Optical Mapping Technology is a method of deciphering a genome's architecture by creating high-resolution, ordered, whole-genome restriction maps from single DNA molecules. (genomeweb.com)
And by analyzing the images … we can put them back together and create a whole genome," or, in essence, a whole-genome restriction map, White said. (genomeweb.com)
For whole-genome sequence assembly and finishing, the Optical Mapping System is complementary to existing second- and forthcoming third-generation sequencing technologies, he said, in that it can provide a complete genome scaffold for contig alignment and orientation. (genomeweb.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)
After raw sequence files are generated (in FASTQ format), quality-checked, and pre-processed in some way, the next step in most NGS pipelines is mapping to a reference genome. (utexas.edu)
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)
results can serve as an important argument in favour of the proposal to develop a special program for sequencing the genomechromosomes 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)
I am thinking that I should use a 'mapping' technique to assemble the genome using the Ecoli O157:H7 genome as a reference, but I have no idea how to do this. (stackexchange.com)
This paper discusses the sequencing of the genome of Arxula adeninivorans, a yeast of biotechnological interest. (biomedcentral.com)
This sequencing bias remains despite the number of recent publications of yeast genome sequences. (biomedcentral.com)
The only disadvantage to this type of library is that it cannot be used for physical mapping or full-genome sequencing. (biost.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)
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)
The genome sequences were assembled from Illumina HiSeq and PacBio sequencing data and verified with the optical mapping data. (cdc.gov)
Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives. (doe.gov)
Contigs French : contigs Group of clones representing overlapping regions of a genome used to determine the physical map of a chromosome region. (findo.com.py)
Chromosome11
A great deal more advantageous than simply YAC-mainly based chromosome libraries will be development of phony filamentous yeast chromosomes (FAG? (viperin.fr)
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)
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)
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)
Molecular and phenotypic mapping of the short arm of chromosome 5: sublocalization of the critical region for the cri-du-chat syndrome. (medscape.com)
A yeast artificial chromosome contig of the critical region for cri-du-chat syndrome. (medscape.com)
This involves taking a FASTA file as input, with each chromosome (or contig) as a separate FASTA entry, and producing an aligner-specific set of files as output. (utexas.edu)
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)
High-resolution physical mapping by combined Alu-hybridization/PCR screening: construction of a yeast artificial chromosome map covering 31 centimorgans in 3p21-p14. (u-tokyo.ac.jp)
5 megabase contig on mouse chromosome 1. (u-tokyo.ac.jp)
1993) Isolation and FISH mapping of 80 cosmid clones on the short arm of human chromosome 3. (u-tokyo.ac.jp)
Genes5
Therefore we believe that during evolution yeasts have developed a sophisticated regulatory system that integrates both TF-based and non-TF based mechanisms(s) for concurrent regulation of neighboring genes in response to various environmental changes. (biomedcentral.com)
A hundred or so yeast family genes have thus far been separated and you may sequenced, also family genetics like those working in glycolysis and you may amino acidic biosynthesis, and some official genetics security enzymes inside, particularly, inside the phone duration, mitosis, or cellular differentiation. (viperin.fr)
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)
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)
The amylolytic yeast Saccharomycopsis fibuligera has served as a good source of enzymes and genes involved in saccharification. (biomedcentral.com)
Chromosomes4
Although hybrids of these two species inherit three chromosomes from each parent, the majority of spores (the yeast equivalent of sperm) that these hybrids produce fail to develop into new yeast cells. (elifesciences.org)
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)
Thus the budding yeast Saccharomyces cerevisiae sports TG 1-3 repeats on the ends of its chromosomes [ 2 ], while telomeres of both the filamentous fungus Neurospora crassa and humans comprise TTAGGG repeats [ 3 , 4 ]. (biomedcentral.com)
This led to the identification of 37 contigs representing 37 chromosomes in N. fowleri. (cdc.gov)
Cosmid1
Direct cosmid-cosmid hybridisation analysis placed subsets of these clones within four different cosmid contigs. (ox.ac.uk)
Genomic4
Finally, normalized contact maps are clustered to construct draft genomic bins. (biomedcentral.com)
Combined with the eight environmental viral contigs from metagenomics, this study helps fill the gap in our understanding of the isolation, genomic and evolutionary development of Oceanospirillum bacteriophages and provides new insights into the interactions between hosts and bacteriophages for these important marine hydrocarbon-degrading microbial populations. (biomedcentral.com)
Maintaining your repository of genomic annotations, sequence and indices for read-mapping software is built-in. (sr.ht)
We have tremendous experience with plant, animal, yeast and bacterial genomic BAC libraries. (biost.com)
Genomes3
By using the information for TF binding sites in promoter regions available from the MYBS database http://cg1.iis.sinica.edu.tw/~mybs/ , the ratios of TF-sharing pairs among all the adjacent pairs in yeast genomes were analyzed. (biomedcentral.com)
Way more yeast variety can benefit out-of YAC tech, especially fungus having massive genomes, for instance the oomycetes, and other intractable fungus. (viperin.fr)
NEW YORK (GenomeWeb News) - As OpGen intensifies the commercialization of its optical mapping technology, it is looking to expand its use to larger genomes, including humans, within the next year, its CEO said. (genomeweb.com)
Species10
Here we identify causes underlying hybrid infertility of two recently diverged fission yeast species Schizosaccharomyces pombe and S. kambucha , which mate to form viable hybrid diploids that efficiently complete meiosis, but generate few viable gametes. (elifesciences.org)
have now looked at two species of fission yeast- S. pombe and S. kambucha -that share 99.5% of their DNA sequence. (elifesciences.org)
Since these two yeast species are so closely related, the findings of Zanders et al. (elifesciences.org)
In order to resolve the evolutionary aspect of this issue, we investigated the conservation of adjacent pairs in five yeast species. (biomedcentral.com)
Our analyses showed that the proportion of adjacent pairs conserved in five yeast species is relatively low compared to that in the mammalian lineage. (biomedcentral.com)
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. (lookformedical.com)
This yeast has been considered one of the best producers of amylolytic enzymes among ascomycetous yeast species [ 3 ], since its capacity to perform starch hydrolysis was first reported by Wickerham et al. (biomedcentral.com)
shows an overview of how the contigs could be classified to availible species from the database. (stackexchange.com)
Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. (biomedcentral.com)
Kurtzmann and Robnett [ 14 ] revisited the phylogeny of yeasts and deduced that Arxula is a member of the Blastobotrys genus that contains both anamorphic and ascosporic species. (biomedcentral.com)
Fission yeast1
The fission yeast S. pombe lacks Sir3p and Sir4p but employs methylation of histone H3 lysine 9 (K9) plus a Sir2p homologue (Sir2) for silencing [ 15 ]. (biomedcentral.com)
Clones1
Mapping of anchor clones from each contig, against the mapping panel, localised all these contigs within the Xq12-q13.1 region. (ox.ac.uk)
Sequence3
An increasing number of GO-mapped sequence databases make it possible to replace traditional database searches with GO-related searches. (biomedcentral.com)
Using OpGen's MapSolver software, contigs generated by sequencers are mapped in silico "so that the contigs can be mapped back to the complete ordered optical map scaffold of DNA, giving researchers the ability to very rapidly orient the sequence data to help accelerate assembly and finishing," he said. (genomeweb.com)
By checking "Create table with statistics for each mapping", a table showing detailed statistics for each reference sequence will be generated (figure 27.24 ). (qiagenbioinformatics.com)
Overall, BLAST analysis performed on assembled T. frezii contigs showed highest similarity (~ 78%) to Anthracocystis flocculosa (Syn. (biomedcentral.com)
Pombe1
Telomeric silencing has been demonstrated in organisms ranging from yeasts to humans (reviewed in [ 9 ]) but it has been best characterized in S. cerevisiae , Schizosaccharomyces pombe and Drosophila melanogaster , organisms that have no, or very little, DNA methylation. (biomedcentral.com)
Genetics1
Along side next several years, additional yeast genetics was sequenced and you will distinguisheded, providing a clearer image of the newest unit mechanisms regarding lifetime in this type of down eukaryotes. (viperin.fr)
Cerevisiae1
The industrially important yeast Blastobotrys (Arxula ) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae . (biomedcentral.com)
Biotechnological1
Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. (biomedcentral.com)
Cosmids1
In addition, cosmids, YAC vectors, and techniques such as for example contig mapping will in all probability facilitate both isolation away from fascinating qualities when you look at the intractable fungi, therefore the unit investigation out of more tractable challenges from inside the deeper depth. (viperin.fr)
Annotation2
Compared to the currently available annotation, we provided more than twice the number of contigs with good quality annotation, and additionally we assigned a confidence value to each predicted GO term. (biomedcentral.com)
Now after you removed unwanted contigs, you can run prokka to get the annotation. (stackexchange.com)
Restriction1
One of the things that we are doing is developing the algorithms and the computational ability to enable that work to take our single-molecule restriction maps that are created and incorporate those and utilize those for the assembly and the gap closure," he said. (genomeweb.com)
Strain2
For strain typing, an optical map of the isolate of interest can be generated in about 24 hours, compared to the days or weeks that it would take with next-generation sequencing-based methods. (genomeweb.com)
When you use a mapping, you must be aware that you may miss relevant and diverged regions because of the mapping to a reference strain. (stackexchange.com)
Fungi2
Saccharomycopsis fibuligera (synonymous with Endomyces fibuligera ), a member of the subphylum Saccharomycotina of the phylum Ascomycota of the Fungi kingdom, is found worldwide as the major amylolytic yeast utilized in indigenous food fermentation using rice and cassava. (biomedcentral.com)
Moreover, this yeast has been isolated as one of spoilage fungi causing chalk mold defects, which are commonly seen on the dark bread that is popular in continental Europe and the UK. (biomedcentral.com)
Extract1
from clinical samples by using buffered charcoal yeast extract (BCYE) medium, with and without antimicrobial drugs, including polymyxin B, cycloheximide, and vancomycin. (cdc.gov)
Contigs are assembled from the shotgun sequencing reads, and paired-end Hi-C reads are mapped to the assembled contigs to generate raw contact maps, which are then normalized to correct the strong experimental biases. (biomedcentral.com)
Dominant1
Even though many mapping tools exist, a few individual programs have a dominant 'market share' of the NGS world. (utexas.edu)
Analysis2
Several new genomics technologies have become available that offer long-read sequencing or long-range mapping with higher throughput and higher resolution analysis than ever before. (nature.com)
Reconstructed carbon and sulfur metabolic pathways, coupled with RNA-Seq analysis, suggested a marginal Crabtree effect under high glucose and activation of sulfur metabolism toward methionine biosynthesis under sulfur limitation in this yeast. (biomedcentral.com)
Cells2
As a dimorphous yeast, S. fibuligera propagates by forming abundantly branched septate hyphae along with typical budding yeast-like cells [ 2 ]. (biomedcentral.com)
To functionally characterize the affinity of OsCYB5-2 sHAK21 for K+ below salt treatment, kinetic parameters (inhibition continuous Ki for Na+) were assessed in yeast cells. (glucagon-receptor.com)
Assembly1
A de novo assembly with spades should work as well as a mapping with bowtie2. (stackexchange.com)
Standard deviation of the distribution of the lengths of all the zero coverage regions on that contig. (qiagenbioinformatics.com)
Optical3
During the spring, the company launched its first instrument, called the Argus LS Optical Mapping System, globally. (genomeweb.com)
The Optical Mapping Technology was licensed from New York University and the University of Wisconsin, and OpGen has been developing it since its founding in 2002. (genomeweb.com)
As a result, mutations, such as insertions, inversions, and deletions that may be missed with sequencing technologies can be found with the Optical Mapping System, and, similarly, contig misassemblies can be identified and corrected. (genomeweb.com)
Strengths1
This is a comprehensive Review of all major sequencing and mapping platforms, including a detailed discussion of their relative strengths and weaknesses. (nature.com)