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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).
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 last 10-12 bases at the 3' end of a primer are sensitive to initiation of polymerase extension and general primer stability on the template binding site. The effect of a single mismatch at these last 10 bases at the 3' end of the primer depends on its position and local structure, reducing the primer binding, selectivity, and PCR efficiency.
The ARB (ARB short for the Latin arbor) program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for nucleic acid and amino acid sequence data.
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
The BLAT Search Genome can accept multiple sequences of the same type at once, up to a maximum of 25. For multiple sequences, the total number of nucleotides must not exceed 50,000 for DNA searches or 25,000 letters for protein or translated sequence searches. An example of searching a target database with a DNA query sequence is shown in Figure 2.
Multiple sequence alignment: align sequences of DNA, RNA, [2] or amino acids. [3] Genome alignment: find and align the syntenic regions of multiple genomes. Oligonucleotide design: [4] primer design [5] [6] for polymerase chain reaction (PCR), probe design for fluorescence in situ hybridization (FISH) [7] or DNA microarrays. [8]