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16S/18S/ITS Amplicon Sequencing-NGS
Amplicon sequencing with Illumina technology, specifically targeting the 16S, 18S, and ITS genetic markers, is a powerful method for unraveling the phylogeny, taxonomy, and species abundance within microbial communities. This approach involves sequencing the hypervariable regions of housekeeping genetic markers. Originally introduced as a molecular fingerprint by Woeses et al in 1977, this technique has revolutionized microbiome profiling by enabling isolation-free analyses. Through the sequencing of 16S (bacteria), 18S (fungi), and Internal Transcribed Spacer (ITS, fungi), researchers can identify not only abundant species but also rare and unidentified ones. Widely adopted as a pivotal tool, amplicon sequencing has become instrumental in discerning differential microbial compositions across diverse environments, including the human mouth, intestines, stool, and beyond.
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Bacterial and Fungal Whole Genome Re-Sequencing
Bacterial and fungal whole-genome re-sequencing projects are pivotal for advancing microbial genomics by enabling the completion and comparison of microbial genomes. This facilitates fermentation engineering, the optimization of industrial processes, and the exploration of secondary metabolism pathways. Furthermore, fungal and bacterial re-sequencing is crucial for understanding environmental adaptation, optimizing strains, and revealing genetic evolution dynamics, with broad implications in medicine, agriculture, and environmental science.
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PacBio-Full-length 16S/18S/ITS Amplicon Sequencing
Amplicon (16S/18S/ITS) platform is developed with years of experience in microbial diversity project analysis, which contains standardized basic analysis and personalized analysis: basic analysis covers the mainstream analysis content of current microbial research, the analysis content is rich and comprehensive, and analysis results are presented in the form of project reports; The content of personalized analysis is diverse. Samples can be selected and parameters can be set flexibly according to the basic analysis report and research purpose, to realize personalized requirements. Windows operating system, simple and fast.
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PacBio-Full-length Transcriptome (Non-Reference)
Taking Pacific Biosciences (PacBio) Isoform sequencing data as input, this App is able to identify full-length transcript sequences (without assembly). By mapping full-length sequences against reference genome, transcripts can be optimized by known genes, transcripts, coding regions, etc. In this case, more accurate identification of mRNA structures, such as alternative splicing, etc, can be achieved. Joint analysis with NGS transcriptome sequencing data enables more comprehensive annotation and more accurate quantification in expression at transcript level, which largely benefits downstream differential expression and functional analysis.
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Reduced Representation Bisulfite Sequencing (RRBS)
Reduced representation bisulfite sequencing (RRBS) relies on the enrichment of CpG island-rich regions by MspI cleavage followed by size selection of 200-500/600 bps fragments. Consequently, only regions proximal to CpG islands are sequenced, while those with distant CpG islands are excluded from the analysis. This process, combined with bisulfite sequencing, allows for high-resolution detection of DNA methylation, and the sequencing approach, PE150, focuses specifically on the ends of the inserts rather than the middle, increasing the efficiency of methylation profiling.
This technique has emerged as a cost-effective and efficient alternative to Whole Genome Bisulfite Sequencing (WGBS) in DNA methylation research. While WGBS provides comprehensive insights by examining the entire genome at single base resolution, its high cost can be a limiting factor, which RRBS strategically mitigates this challenge by selectively analyzing a representative portion of the genome. This methodology is an invaluable tool that enables cost-effective DNA methylation research and advances knowledge of epigenetic mechanisms.
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Prokaryotic RNA Sequencing
RNA sequencing empowers the comprehensive profiling of all RNA transcripts within cells under specific conditions. This cutting-edge technology serves as a potent tool, unveiling intricate gene expression profiles, gene structures, and molecular mechanisms associated with diverse biological processes. Widely adopted in fundamental research, clinical diagnostics, and drug development, RNA sequencing offers insights into the intricacies of cellular dynamics and genetic regulation. Our prokaryotic RNA sample processing is tailored for prokaryotic transcriptomes, involving rRNA depletion and directional library preparation.
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Metatranscriptome Sequencing
Leveraging Illumina sequencing technology, BMKGENE’s metatranscriptome sequencing service unveils the dynamic gene expression of a diverse array of microbes, spanning eukaryotes to prokaryotes and viruses, within natural environments such as soil, water, sea, stool, and the gut. Our comprehensive service empowers researchers to delve into complex microbial communities’ complete gene expression profiles. Beyond taxonomic analysis, our metatranscriptome sequencing service facilitates exploration into functional enrichment, shedding light on differentially expressed genes and their roles. Uncover a wealth of biological insights as you navigate the complex landscapes of gene expression, taxonomic diversity, and functional dynamics within these diverse environmental niches.
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De novo Fungal Genome Assembly
BMKGENE offers versatile solutions for fungal genomes, catering to diverse research needs and desired genome completeness. Utilizing short-read Illumina sequencing alone allows the generation of a draft genome. Short-reads and long-read sequencing using Nanopore or Pacbio are combined for a more refined fungal genome with longer contigs.
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Toolkits
BMKCloud is a leading bioinformatic platform providing one-stop solution for genomic programs, which is widely trusted by researchers in various arena including medical, agricultural, environmental, etc. BMKCloud is committed to provide integrated, reliable and efficient services including bioinformatic analysis platforms and tools, computing resources, public database, bioinformtic online courses, etc. BMKCloud has various frequently used bioinformatic tools of including gene annotation, evolutionary genetic tools, ncRNA, data quality control, assembly, alignment, data extraction, mutations, statistics, figure generator, sequence analysis,etc.
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De novo Bacterial Genome Assembly
We provide a complete bacterial genome assembly service, guaranteeing 0 gaps. This is possible by integrating long-read sequencing technologies, such as Nanopore and PacBio for assembly and short-read sequencing with Illumina for assembly validation and error correction of ONT reads. Our service provides the complete bioinformatic workflow from assembly, functional annotation, and advanced bioinformatic analysis, fulfilling specific research goals. This service enables the development of precise reference genomes for various genetic and genomic studies. Additionally, it forms the basis for applications such as strain optimization, genetic engineering, and microbial technology development, ensuring reliable and gap-free genomic data crucial for advancing scientific insights and biotechnological innovation.
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Small RNA
Small RNAs are type of short non-coding RNA with average length of 18-30 nt, including miRNA, siRNA and piRNA. These small RNAs have been massively reported to be involved in various biological processes such as mRNA degradation, translation inhibition, heterochromatin formation, etc. SmallRNA sequencing analysis has been widely applied in studies on animal/plant development, disease, virus, etc. Small RNA sequencing analysis platform consists of standard analysis and advanced data mining. On base of RNA-seq data, standard analysis can achieve miRNA identification and prediction, miRNA target gene prediction, annotation and expression analysis. Advanced analysis enables customized miRNA search and extraction, Venn diagram generation, miRNA and target gene network building.
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NGS-WGS (Illumina/BGI)
NGS-WGS is an whole genome re-sequencing analysis platform, which is developed on base of rich experience in Biomarker Technologies. This ease-to-use platform allows quick submission of an integrated analysis workflow by simply setting a few basic parameter, which fits for DNA sequencing data generated from both Illumina platform and BGI sequencing platform. This platform is deployed on high performance computing server, which empowers highly efficient data analysis in very limited time. Personalized data mining is available on base of standard analysis, including mutated gene query, PCR primer design, etc.
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mRNA(Reference)
Transcriptome is the link between genomic genetic information and the proteome of biological function. Transcriptional level regulation is the most important and the most widely studied regulation mode of organisms. Transcriptome sequencing can sequence the transcriptome at any point in time or under any condition, with a resolution accurate to a single nucleotide.It can dynamically reflect the level of gene transcription, simultaneously identify and quantify rare and normal transcripts, and provide the structural information of sample specific transcripts.
At present, transcriptome sequencing technology has been widely used in agronomy, medicine and other research fields, including animal and plant development regulation, environmental adaptation, immune interaction, gene localization, species genetic evolution and tumor and genetic disease detection.
