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Found 7 result(s)
Intrepid Bioinformatics serves as a community for genetic researchers and scientific programmers who need to achieve meaningful use of their genetic research data – but can’t spend tremendous amounts of time or money in the process. The Intrepid Bioinformatics system automates time consuming manual processes, shortens workflow, and eliminates the threat of lost data in a faster, cheaper, and better environment than existing solutions. The system also provides the functionality and community features needed to analyze the large volumes of Next Generation Sequencing and Single Nucleotide Polymorphism data, which is generated for a wide range of purposes from disease tracking and animal breeding to medical diagnosis and treatment.
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Using serial analysis of gene expression (SAGE) and microarrays, we are examining total mRNA populations in all developmental stages, both in whole worms and in specific cells and tissues. In addition, we are building promoter::GFP constructs to monitor gene expression in transgenic worms, focusing on C. elegans genes that have human orthologues. Also available are web-based PCR primer design tools, and access to information about our C. elegans Fosmid library.
dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library. Most EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format. dbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or in small batches. Among these sequences are products of differential display experiments and RACE experiments. The thing that these sequences have in common with traditional ESTs, regardless of length, quality, or quantity, is that there is little information that can be annotated in the record. If a sequence is later characterized and annotated with biological features such as a coding region, 5'UTR, or 3'UTR, it should be submitted through the regular GenBank submissions procedure (via BankIt or Sequin), even if part of the sequence is already in dbEST. dbEST is reserved for single-pass reads. Assembled sequences should not be submitted to dbEST. GenBank will accept assembled EST submissions for the forthcoming TSA (Transcriptome Shotgun Assembly) division. The individual reads which make up the assembly should be submitted to dbEST, the Trace archive or the Short Read Archive (SRA) prior to the submission of the assemblies.
Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research. Xenbase also provides a critical data sharing infrastructure for many other NIH-funded projects, and is a focal point for the Xenopus community. In addition to our primary goal of supporting Xenopus researchers, Xenbase enhances the availability and visibility of Xenopus data to the broader biomedical research community.
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GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.