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Most Ensembl Genomes data is stored in MySQL relational databases and can be accessed by the Ensembl REST interface, the Perl API, Biomart or online. [5] Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public. [6] Ensembl and Ensembl Genomes software uses an Apache 2.0 license [7] license.
In the Ensembl project, sequence data are fed into the gene annotation system (a collection of software "pipelines" written in Perl) which creates a set of predicted gene locations and saves them in a MySQL database for subsequent analysis and display. Ensembl makes these data freely accessible to the world research community.
The background indicates the symbol sources: HGNC Approved Genes, EntrezGene Database, Ensembl Gene Database, or GeneCards Generated Genes. Aliases: Aliases, as its name indicates, shows synonyms and aliases of the gene according to diverse sources such as HGNC. The right column displays how the aliases associated with the resources and gives ...
The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes [8] [9] EuGene: Integrative gene finding: Prokaryotes, Eukaryotes [10] [11] FGENESH: HMM-based gene structure prediction: multiple genes, both chains: Eukaryotes [12] FrameD: Find genes and frameshift in G+C rich prokaryote ...
NCBI:Ensembl protein length different: Checks if the protein encoded by the NCBI RefSeq is the same length as the EBI/WTSI protein NCBI:Ensembl low percent identity: Checks for >99% overall identity between the NCBI and EBI/WTSI proteins Gene discontinued: Checks if the GeneID is no longer valid
70612 Ensembl ENSG00000089063 ENSMUSG00000027341 UniProt Q96A57 Q8CIB6 RefSeq (mRNA) NM_001009923 NM_001009924 NM_001009925 NM_014145 NM_001330984 NM_001330985 NM_001330986 NM_001330987 NM_001141971 NM_027478 RefSeq (protein) NP_001009923 NP_001009924 NP_001009925 NP_001317913 NP_001317914 NP_001317915 NP_001317916 NP_054864 NP_001135443 NP_081754 Location (UCSC) Chr 20: 5.07 – 5.11 Mb Chr 2 ...
Gene prediction is a misleading term, as most gene predictors only identify coding sequences (CDS) and do not report untranslated regions (UTRs); for this reason, CDS prediction has been proposed as a more accurate term. [24]
Single nucleotide polymorphism annotation (SNP annotation) is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query.