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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 NCBI assigns a unique identifier (taxonomy ID number) to each species of organism. [5] The NCBI has software tools that are available through web browsers or by FTP. For example, BLAST is a sequence similarity searching program. BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds.
There are variations within Kozak consensus sequence, such as G or A is observed three nucleotides upstream (at position -3) of AUG. Bases between positions -3 and +4 of Kozak sequence have the most significant impact on translational efficiency. Hence, a sequence (A/G)NNAUGG is defined as a strong Kozak signal in the CCDS project.
The reference sequence belongs to European haplogroup H2a2a1. The revised CRS is designated as rCRS. It is deposited in the GenBank NCBI database under accession number NC_012920. [1] When mitochondrial DNA sequencing is used for genealogical purposes, the results are often reported as differences from the revised CRS. The CRS is a reference ...
The first printout of the human reference genome presented as a series of books, displayed at the Wellcome Collection, London. A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of the set of genes in one idealized individual organism of a species.
These three databases are primary databases, as they house original sequence data. They collaborate with Sequence Read Archive (SRA), which archives raw reads from high-throughput sequencing instruments. Secondary databases are: [clarification needed] 23andMe's database; HapMap; OMIM (Online Mendelian Inheritance in Man): inherited diseases; RefSeq
In this example there is an NCBI-assigned identifier, and the description holds the original identifier from Solexa/Illumina (as described above) plus the read length. Sequencing was performed in paired-end mode (~500bp insert size), see SRR001666. The default output format of fastq-dump produces entire spots, containing any technical reads and ...
Slider is an application for the Illumina Sequence Analyzer output that uses the "probability" files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Yes Yes No No [53] [54] 2009-2010 SOAP, SOAP2, SOAP3, SOAP3-dp SOAP: robust with a small (1-3) number of gaps and mismatches.