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Some tools available to bulk RNA-Seq are also applied to single cell analysis, however to face the specificity of this technique new algorithms were developed. CEL-Seq [114] single-cell RNA-Seq by multiplexed linear amplification. Drop-Seq [115] Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
The fundamental aspect of BRB-seq is the optimized sample barcode primers. Each barcoded nucleotide sequence includes an adaptor for primer annealing, a 14-nt long barcode that assigns a unique identifier to each individual RNA sample, and a random 14-nt long UMI that tags each mRNA molecule with a unique sequence to distinguish between original mRNA transcripts and duplicates that result from ...
EzTaxon-e: database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences NCBI Taxonomy: a taxonomic database operated by NCBI and concentrating on all taxa for which DNA sequences are available (those sequences are stored by GenBank , another database operated by NCBI).
A catalog of human long poly-adenylated RNA transcripts derived from computational analysis of high-throughput RNA-Seq data from over 6,500 samples, spanning diverse cancer and tissue types [13] slncky Evolution Browser: This site contains alignments and evolutionary metrics of conserved lncRNAs. [14] Cancer LncRNA Census (CLC)
Automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences Eukaryotes [1] FragGeneScan: Predicting genes in complete genomes and sequencing Reads: Prokaryotes, Metagenomes [2] ATGpr: Identifies translational initiation sites in cDNA sequences: Human [3] Prodigal
The Rfam database can be used for a variety of functions. For each ncRNA family, the interface allows users to: view and download multiple sequence alignments; read annotation; and examine species distribution of family members. There are also links provided to literature references and other RNA databases.
RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5' and 3' gene boundaries. Recent advances in RNA-Seq include single cell sequencing, bulk RNA sequencing, [6] 3' mRNA-sequencing, in situ sequencing of fixed tissue, and native RNA molecule sequencing with single-molecule real-time sequencing. [7]
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