island genome plays an important role in the evolution of microbial genomes, providing a mechanism for the strain to adapt to new ecological conditions. Various methods of computing, both genome-based composition and comparative, has been developed to identify them. Some of these methods are explicitly designed to work in a single strain, while others use multiple strains. In general, the existing methods do not identify the island in phylogeny context in which they evolved. Even some of the most suitable strain approach to identify genomic islands that are present in one strain but not in others. They do not automatically recognize the island which is shared between multiple strains in clade, or branch determines that these islands were included in the phylogenetic tree.
We have developed a software package, xenoGI, which identifies genomic islands and map their origin in clade is closely related bacteria, determine their branches put on. It takes as input a set of genome sequencing and trees determine their phylogenetic relationships. Makes heavy use synteny information, package builds a gene family by way of tree species-conscious, and then attempt to merge into the islands of the families whose members are close together and the most recent common ancestor shared.
This package provides a variety of text-based analysis functions, as well as the ability to export the island genome into a suitable format to look at the genome browser. We demonstrate the ability of a package with some examples of enteric bacteria, including the examination of fitness island evolution in the genus Escherichia acid. In addition we use the output of the simulation and a set of genomic islands known from the literature to show that xenoGI can accurately identify genomic islands and place them on a phylogenetic tree.
xenoGI is an effective tool for studying the history of the island inserts in clade microbial genomes. This identifies a genomic island, and determine their branches included in the phylogenetic tree for the clade. Such information is valuable because it helps us understand the adaptive road which has resulted in species live.
xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria.
15 years of the GDR: new data and functionality in the Genome Database for Rosaceae.
Genome Database for Rosaceae is a web-based integrated community resource database that provides access to publicly available genomics, genetics and breeding of data and data mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in the GDR has increased tremendously over the last 5 years. GDR now houses several versions of the entire genome assembly data and explanation of the 14 species, provided by recent advances in sequencing technology. reference transcriptome sought, RefTrans, combining peer-reviewed and published RNA-Seq datasets described EST and, newly available for major crop species.
Significantly more quantitative trait loci, the genetic maps and markers are available in MapViewer, a new visualization tool that integrates better with other pages in the GDR. Preparation can be accessed via the new GDR Cyc track database, and the latest genome synteny between assemblies of eight species can be seen through the new synteny browser, SynView. Compiled single nucleotide polymorphisms diversity of data and phenotypic data from publicly available dataset farms integrated with other relevant data.
Description: His tagged recombinant yeast AHA1 Protein expressed in E. coli for WB, SDS-PAGE, Functional Assay. The biological activity of this protein has not yet been tested.
Description: His tagged recombinant yeast AHA1 Protein expressed in E. coli for WB, SDS-PAGE, Functional Assay. The biological activity of this protein has not yet been tested.
Description: His tagged recombinant yeast AHA1 Protein expressed in E. coli for WB, SDS-PAGE, Functional Assay. The biological activity of this protein has not yet been tested.
Description: GLC8 Yeast (Saccharomyces cerevisiae) Recombinant produced in E.coli is a single, glycosylated polypeptide chain containing 265 amino acids (1-229) and having a molecular mass of 30.7 kDa (molecular size on SDS-PAGE will appear higher). ;The GLC8 is fused to a 35 amino acid His Tag at N-Terminus and purified by standard chromatography techniques.
Description: Proteases (also called Proteolytic Enzymes, Peptidases, or Proteinases) are enzymes that hydrolyze the amide bonds within proteins or peptides. Most proteases act in a specific manner, hydrolyzing bonds at or adjacent to specific residues or a specific sequence of residues contained within the substrate protein or peptide. Proteases play an important role in most diseases and biological processes including prenatal and postnatal development, reproduction, signal transduction, the immune response, various autoimmune and degenerative diseases, and cancer. They are also an important research tool, frequently used in the analysis and production of proteins. Kex-2 cleaves at the carboxyl end of the recognition sequences Arg-Arg/X and Lys-Arg/X. Recombinant Yeast Kex-2 is a 59.9 kDa protease consisting of 554 amino acid residues.
Description: Proteases (also called Proteolytic Enzymes, Peptidases, or Proteinases) are enzymes that hydrolyze the amide bonds within proteins or peptides. Most proteases act in a specific manner, hydrolyzing bonds at or adjacent to specific residues or a specific sequence of residues contained within the substrate protein or peptide. Proteases play an important role in most diseases and biological processes including prenatal and postnatal development, reproduction, signal transduction, the immune response, various autoimmune and degenerative diseases, and cancer. They are also an important research tool, frequently used in the analysis and production of proteins. Kex-2 cleaves at the carboxyl end of the recognition sequences Arg-Arg/X and Lys-Arg/X. Recombinant Yeast Kex-2 is a 59.9 kDa protease consisting of 554 amino acid residues.
Description: Protoplast secreted protein 1 (Pst1) is an anchored plasma membrane protein. Pst1 was previously identified as a protein secreted by yeast regenerating protoplasts, which suggests a role in cell wall construction (1). Pst1 is a protein with 444 amino acids and is attached to yeast cell wall via a glycosylphosphatidylinisotol (GPI) anchor (2). Pst1 contains 15 potential N-linked glycosylation sites and is heavily glycosylated. It migrates at around 200 kDa on SDS-PAGE when produced in wild type S. cerevisiae. Our Pst1 protein was expressed in a genetically manipulated triple-mutant (TM) S. cerevisiae stain (Δoch1 Δmnn1 Δmnn4), which results in the production of sole Man8GlcNAc2 carbohydrate structures and Pst1 migration at approximately 100 kDa. When produced in the TM yeast, Pst1 can be recognized by several HIV-1 broadly neutralizing antibodies, including 2G12 and recently identified glycan-specific PGT antibodies (3). Among several heavily N-glycosylated TM yeast glycoproteins, Pst1 shows high affinity for 2G12 and efficiently inhibits gp120 interactions with 2G12 and DC-SIGN, and it also blocks 2G12-mediated neutralization of HIV-1 pseudoviruses (4).
Description: Proteases (also called Proteolytic Enzymes, Peptidases, or Proteinases) are enzymes that hydrolyze the amide bonds within proteins or peptides. Most proteases act in a specific manner, hydrolyzing bonds at or adjacent to specific residues or a specific sequence of residues contained within the substrate protein or peptide. Proteases play an important role in most diseases and biological processes including prenatal and postnatal development, reproduction, signal transduction, the immune response, various autoimmune and degenerative diseases, and cancer. They are also an important research tool, frequently used in the analysis and production of proteins. Kex-2 cleaves at the carboxyl end of the recognition sequences Arg-Arg/X and Lys-Arg/X. Recombinant Yeast Kex-2 is a 60.4 kDa protease consisting of 558 amino acid residues.
Description: LIF Human Recombinant produced in yeast is a single, glycosylated polypeptide chain containing 180 amino acids and having a molecular mass of 58.5 kDa. The LIF is purified by proprietary chromatographic techniques.
Description: Glutaredoxin-2 Saccharamyces cerevisiae Recombinant containing 6x His tag at C-terminus produced in E.Coli is a single, non-glycosylated, Polypeptide chain having a molecular mass of 17 kDa.
Description: Glutaredoxin Saccharamyces cerevisiae Recombinant containing 6x His tag at C-Terminus produced in E.Coli is a single, non-glycosylated, Polypeptide chain having a molecular mass of 16 kDa.
Description: Insulin Human Recombinant produced in Yeast is a two chain, glycosylated polypeptide chain containing 51 amino acids and having a molecular mass of 5807 Dalton. Zinc content was found to be 0.4%. Insulin is purified by proprietary chromatographic techniques.
Also, the new Breeding Management Information System allows breeders to upload, manage and analyze data in their personal breeding GDR secure server with an option to release public data.
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