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  2. Sequence alignment - Wikipedia

    en.wikipedia.org/wiki/Sequence_alignment

    Alignment of 27 avian influenza hemagglutinin protein sequences colored by residue conservation (top) and residue properties (bottom) Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple alignment methods try to align all of the sequences in a given query set.

  3. Multiple sequence alignment - Wikipedia

    en.wikipedia.org/wiki/Multiple_sequence_alignment

    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.

  4. Gap penalty - Wikipedia

    en.wikipedia.org/wiki/Gap_penalty

    Therefore, using a good gap penalty model will avoid low scores in alignments and improve the chances of finding a true alignment. [3] In genetic sequence alignments, gaps are represented as dashes(-) on a protein/DNA sequence alignment. [1] Unix diff function - computes the minimal difference between two files similarly to plagiarism detection.

  5. Sequence homology - Wikipedia

    en.wikipedia.org/wiki/Sequence_homology

    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 ...

  6. Smith–Waterman algorithm - Wikipedia

    en.wikipedia.org/wiki/Smith–Waterman_algorithm

    The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of looking at the entire sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.

  7. BLAT (bioinformatics) - Wikipedia

    en.wikipedia.org/wiki/BLAT_(bioinformatics)

    Alignment of multiple mRNA sequences onto a genome assembly in order to infer their genomic coordinates; [10] Alignment of a protein or mRNA sequence from one species onto a sequence database from another species to determine homology. Provided the two species are not too divergent, cross-species alignment is generally effective with BLAT.

  8. Sequence analysis - Wikipedia

    en.wikipedia.org/wiki/Sequence_analysis

    Example multiple sequence alignment. There are millions of protein and nucleotide sequences known. These sequences fall into many groups of related sequences known as protein families or gene families. Relationships between these sequences are usually discovered by aligning them together and assigning this alignment a score. There are two main ...

  9. List of alignment visualization software - Wikipedia

    en.wikipedia.org/wiki/List_of_alignment...

    The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature.