TB-SEQ, Inc. is a life-science company devoted to the development and application of experimental and computational procedures for functional (meta)genomics analysis of prokaryotic and eukaryotic organisms and communities based on the ribosome profiling NGS platform technology (RIBO-seq) and on computational analysis of sequencing data. TB-Seq develops new experimental protocols and bioinformatics tools applicable to different biological system, and offers related services. Our team combines decades of experience in research and development in computational sequence analysis, molecular biology and biochemistry, in experimental analysis of nucleic acids, and in protein and nucleic acid sequence and structure computational analysis.
TB-SEQ Inc. is resident at the qb3@953 incubator, located at the core of the San Francisco peninsula Biotech hub and in close proximity to the UCSF Mission Bay Campus and facilities.
TB-SEQ is the only commercial provider of RIBO-seq analysis. We offer competitive pricing, fast turn-around, highest quality of execution, and customized project design and execution to fit your needs from data collection, through data analysis, to result summary and high-quality pictures for publication purposes.
Our team has combined decades of experience in scientific research and can assist you in creating a robust and effective experimental design. We will discuss with you the most appropriate experimental strategy and applications of ribosome-profiling techniques in relation to your samples, your scientific/development goals, and your budget. We are specialized in projects focused in functional genomics analysis utilizing the RIBO-seq platform.
We provide cost effective consultation on experimental design for functional genomics projects based on the RIBO-seq platform. We will be glad to discuss with you your project details.
RIBO-seq library preparation
We are experienced in isolating ribosome-bound mRNA from bacterial and eukaryotic cells, and from animal and plant tissues. We have developed sample-specific efficient protocols for all steps of the RIBO-seq procedure, from lysis to library preparation, that allow us to create RIBO-seq libraries of the highest quality from the smallest amount of starting material.
Our proprietary optimized RIBO-seq protocols allow us to produce RIBO-seq libraries of the highest quality more efficiently and with enhanced sensitivity compared to competing protocols.
You provide your frozen cell or tissue samples, and TB-SEQ carries out the entire RIBO-seq library preparation, including cell lysis, monosome isolation and purification, rRNA depletion, gel-isolation of ribosome-bound RNA fragments, cDNA synthesis from the isolated RNA and library prep. for Illumina sequencing. We offer sequencing services through a third party or we deliver the library to you for sequencing through your favorite provider. Turn around time is usually 3-4 weeks for library preparation and one week for sequencing. Upon request we provide standard and customized bioinformatics analysis. We perform standard bioinformatics analysis (mapping of RIBO-seq reads to genome sequence and library-quality assessment based on meta-gene 3-base periodicity and rRNA contamination assessment) (one week turn-around). We will be happy to discuss with you customized bioinformatics and statistical analyses.
Please inquire for a quote.
All information is subject to change without notice. Please contact TB-SEQ Inc. for latest pricing and terms.
We will be glad to prepare RNA-seq libraries in parallel to RIBO-seq libraries upon request. Comparing RNA-seq to RIBO-seq results allows to measure "translation efficiency", i.e., rate of translation per mRNA unit.
We have partnered with sequencing facilities that guarantee fast sequencing services on Illumina HiSeq or MiSeq sequencers.
Bioinformatics analysis of NGS data
Our preprocessing pipeline allows precise quality control and 3'-adaptor and poly-A sequence trimming for maximal data-integrity preservation.
We use the fastest alignment algorithms to characterize perfect, approximate, unique, multiple and discarded read alignment. We work with you to align reads to your favorite reference sequence (genomic or otherwise). We also offer alignment of ribosome footprints to RNA-seq reads for congruency analysis.
New Protein/Peptide and Alternative Translation Initiation Site identification
We have developed proprietary computational tools for the effective identification, analysis, and graphical representation of patterns of protein translation of potential interest, including differential translation, use of alternative TIS, uORF, and AltORF identification.
Differential Gene Expression
We utilize the latest statistical tools for assessing differences in gene expression (RNA-sequencing data) and protein expression (RIBO-sequencing data) across conditions accounting for over-dispersion of sequencing data, including PERMANOVA analysis, negative-binomial fitting, Log-normal fitting and Bayesian inference, and sampling the distribution of the statistics from replicates of experimental samples. Summary data on gene and protein relative expression are provided.
Gene ontology and pathway analysis
Including GSEA gene set enrichment and Leading Edge analyses, Impact Analysis (ROntoTools) and iPathwayGuide.
We have the computational capabilities to perform customized analyses on your sequencing data, using available software packages, our suite of bioinformatics tools, or by developing new analytical tools according to your needs. Whatever the information you are looking to extract from your data, we will be happy to discuss with you the most appropriate computational-analysis design, and to execute it for you.
Bioinformatics for metagenomic functional analysis
TB-SEQ Bioinformatics offers high-end robust bioinformatics to optimize analysis of the information provided by microbiome studies. TB-SEQ Bioinformatics uses the most highly rated software packages for all bioinformatics analyses, as well as proprietary software developed by TB-SEQ scientists for statistical comparative analysis of compositional and functional properties of the microbiome communities, including state-of-the-art measures of phylogenetic and functional diversity. The TB-SEQ's proprietary FunDive software pipeline for statistical analysis of diversity provides statistical analysis of beta diversity (pair-wise weighted, unweighted, and generalized UniFrac, as well as true global beta diversity). Furthermore, FunDive provides a detailed statistical assessment of relative-representation across communities of more than 800 individual functional pathways from the MetaCyc database, and associated taxa. The TB-SEQ bioinformatics team specializes in creative visualization methods to effectively represent compositional properties of microbiome communities.
Alpha and beta phylogenetic diversity and functional diversity based on phylogenetic relations and on MetaCyc pathway representation in 15,000 reference prokaryotic genomes.
Statistical analysis of functional diversity accounting for uncertainty in taxonomic assignment and intra-group variability, by functional pathway.
Rarefactions, rank abundance plots, relative abundance bar plots, etc., in publication ready figures.
Classification of specific marker-based microbial diversity assays (e.g. 16S, 18S, ITS, SSU, etc…)
Classification of shotgun library-based metagenomic diversity analysis to the strain level.
Metagenome taxonomic annotation (MG-RAST, KRAKEN).
Metatranscriptome assembly (Rockhopper 2, Trinity)
Mothur, QIIME, PICRUSt, Explicet, Nephele metagenome analyses.
Custom pipeline and software creation.
Taxonomic Annotation including 16S rRNA and non-16S taxonomic annotation.
Functional Annotation by matching it against microbial entries in pathway/genome databases (MG-RAST).
Pathway Annotation by MetaCyc metabolic pathways (FunDive).
Our team works side-by-side with each client to understand their research questions and to ensure alignment in the study objectives.
For a quote on our services please fill out the form below or visit us on ScienceExchange: