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In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. [1] Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix.
The NCBI assigns a unique identifier (taxonomy ID number) to each species of organism. [5] The NCBI has software tools that are available through internet 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.
In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. [1] This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. [1]
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [2] [3] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4]
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences.
In the DIAMOND [12] +MEGAN [13] approach, all reads are first aligned against a protein reference database, such as NCBI-nr, and then the resulting alignments are analyzed using the naive LCA algorithm, which places a read on the lowest taxonomic node in the NCBI taxonomy that lies above all taxa to which the read has a significant alignment ...
BLAT can be used to align DNA sequences as well as protein and translated nucleotide (mRNA or DNA) sequences. It is designed to work best on sequences with great similarity. The DNA search is most effective for primates and the protein search is effective for land vertebrates.
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene ...