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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).
Brain RNA-Seq [160] An RNA-Seq transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. FusionCancer [161] a database of cancer fusion genes derived from RNA-seq data. Hipposeq a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.
RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.
The Reference Sequence (RefSeq) database [1] is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. RefSeq was introduced in 2000.
The EMBL Nucleotide Sequence Database (EMBL-Bank) has increased in size from around 600 entries in 1982 to over 2.5×10 8 by December 2012. [16] The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) is the section of the ENA which contains high-level genome assembly details, as well as assembled sequences and their functional annotation.
BLAST's nucleotide alignment program, slow and not accurate for short reads, and uses a sequence database (EST, Sanger sequence) rather than a reference genome. BLAT: Made by Jim Kent. Can handle one mismatch in initial alignment step. Yes, client-server Proprietary, freeware for academic and noncommercial use [36] 2002 Bowtie
A sequence profiling tool in bioinformatics is a type of software that presents information related to a genetic sequence, gene name, or keyword input. Such tools generally take a query such as a DNA, RNA, or protein sequence or ‘keyword’ and search one or more databases for information related to that sequence.
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.