Homology inference is important for evolutionary biology and mainly based on a significant sequence similarity, which, in general, is a good indicator of homology. The algorithm has also been designed to take advantage of in order to gene conservation as an indication of homologous regions. We have developed GenFamClust method is based on the quantification of both the conservation of gene order and sequence similarity.
In this study, we validate GenFamClust by comparing homology inference algorithms well known in synthetic dataset. We apply some popular clustering algorithms in homologs concluded by GenFamClust and other algorithms on datasets metazoan and study the results.
Accuracy, equality, interdependence, and other characteristics were investigated for a family of genes produced by a clustering algorithm. GenFamClust also applied to genes from a set of complete fungal genome and gene families that deduced using clustering. The resulting gene families compared with the gold standard of manually curated pillar of Yeast Gene Order Browser. We found that the gene-sequence component GenFamClust simple, yet biologically realistic, and local information for homologous synteny catch.
Research shows that GenFamClust pipe is more accurate, information, and comprehensive to draw conclusions and family homologs of genes and gene-family homology inference method more commonly used. Salmonids is a ray-finned fish that are 11 genera and at least 70 species, including Atlantic salmon, whitefishes, graylings, rainbow trout, and char.
The ancestors of all Salmonidae experience a whole genome duplication (WGD) ~ 80 million years ago, which resulted in the genome autotetraploid. rediplodization genomic still occur in salmonid species, providing a unique system for studying the consequences of the evolution of the whole genome duplication. In recent years, high-quality genome sequence of the Atlantic salmon and rainbow trout has been formed, because the values of their scientific and commercial. In this paper we introduce SalmoBase molecular tools for creating resources for salmonids publicly available in order visualization and analytic tools.
GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm.
Synteny Portal: a web-based portal application for the analysis of synteny blocks.
The latest advances in next-generation sequencing technologies and genome assembly algorithms have allowed the accumulation of a large volume of genome sequences from different species. It has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are regions of the genome conserved among several species, is key to understanding the genome architecture and history of the evolution of genomes. However, the construction and visualization of synteny blocks from several species are very challenging, especially for a biologist with the lack of computing skills.
Here, we present Synteny Portal, a web-based portal application versatility to build, visualize and browse the synteny blocks. With Synteny Portal, users can easily (i) block build synteny between species using alignments prebuilt at UCSC database of genome browser, (ii) visualizing and downloading relationship syntenic as high quality images, (iii) block browse synteny with genetic information, and (iv) to download the details of synteny blocks to be used as input for downstream synteny-based analysis, all within a web-based interface that is intuitive and easy to use.
Description: This mAb shows specificity to E. coli O157 in a simple ELISA. Escherichia coli are Gram negative bacterium that are commonly found in the lower intestine of warm-blooded organisms (endotherms). Their serological types are determined in combination with somatic antigens (O group: O1-O173) and flagella antigens (H type: H1-H56). The E. coli that cause intestinal infectious diseases including diarrhea, acute gastritis or colitis are referred to as pathogenic E. coli, which are classified into the following four groups according to differences in the mode of pathogenicity; enteropathogenic E. coli (EPEC), enteroinvasive E. coli (EIEC), enterotoxigenic E. coli (ETEC) and enterohemorrhagic E. coli (EHEC). Although the identification of pathogenic E. coli requires verification of their pathogenicity, pathogenic E. coli often have specific serotypes; therefore, typing of the serogroup and serotype is necessary in screening pathogenic E. coli.
Description: This mAb shows specificity to E. coli O157 in a simple ELISA. Escherichia coli are Gram negative bacterium that are commonly found in the lower intestine of warm-blooded organisms (endotherms). Their serological types are determined in combination with somatic antigens (O group: O1-O173) and flagella antigens (H type: H1-H56). The E. coli that cause intestinal infectious diseases including diarrhea, acute gastritis or colitis are referred to as pathogenic E. coli, which are classified into the following four groups according to differences in the mode of pathogenicity; enteropathogenic E. coli (EPEC), enteroinvasive E. coli (EIEC), enterotoxigenic E. coli (ETEC) and enterohemorrhagic E. coli (EHEC). Although the identification of pathogenic E. coli requires verification of their pathogenicity, pathogenic E. coli often have specific serotypes; therefore, typing of the serogroup and serotype is necessary in screening pathogenic E. coli.
Description: This mAb shows specificity to E. coli O157 in a simple ELISA. Escherichia coli are Gram negative bacterium that are commonly found in the lower intestine of warm-blooded organisms (endotherms). Their serological types are determined in combination with somatic antigens (O group: O1-O173) and flagella antigens (H type: H1-H56). The E. coli that cause intestinal infectious diseases including diarrhea, acute gastritis or colitis are referred to as pathogenic E. coli, which are classified into the following four groups according to differences in the mode of pathogenicity; enteropathogenic E. coli (EPEC), enteroinvasive E. coli (EIEC), enterotoxigenic E. coli (ETEC) and enterohemorrhagic E. coli (EHEC). Although the identification of pathogenic E. coli requires verification of their pathogenicity, pathogenic E. coli often have specific serotypes; therefore, typing of the serogroup and serotype is necessary in screening pathogenic E. coli.
Human Carbonic Anhydrase II Protein (Ser 2-Lys 260) (E. coli) [His]
Description: This product includes all the kit components in E. coli DNA Primase Assay Kit (Catalog No. EGA100K ) plus 45 ul of 100 x E. coli primase-helicase complex. It is for 100 assays of E.coli DNA primase reactions in a 96-well plate format or 200 assays in 384-well assay format.
E. coli RNA polymerase Assay Kit Plus (E. coli RNA polymerase included)
Description: This product includes all the reagents in E. coli RNA Polymerase Assay Kit (Catalog number RPA100K) plus the enzyme, 33 ul of 100 x E. coli RNAP. It is for 100 assays of E. coli RNA polymerase reactions in a 384-well assay format.
Escherichia coli Serotype O2 (E. coli O2) Antibody
Description: Primary antibody against E. coli O157 (9.88),PerCP conjugate, Concentration: 0.1mg/mL
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We believe that Synteny portal will serve as a very valuable tool that will enable biologists to easily perform comparative genomic studies with the compensation limitations of existing tools. Synteny Portal is freely available on http://bioinfo.konkuk.ac.kr/synteny_portal.
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