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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 .
There are two main types of sequence alignment. Pair-wise sequence alignment only compares two sequences at a time and multiple sequence alignment compares many sequences. Two important algorithms for aligning pairs of sequences are the Needleman-Wunsch algorithm and the Smith-Waterman algorithm. Popular tools for sequence alignment include:
MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is a computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain. The method was published by Robert C. Edgar in two papers in 2004. The first paper, published in Nucleic Acids Research, introduced the sequence alignment algorithm ...
Hybrid methods, known as semi-global or "glocal" (short for global-local) methods, search for the best possible partial alignment of the two sequences (in other words, a combination of one or both starts and one or both ends is stated to be aligned). This can be especially useful when the downstream part of one sequence overlaps with the ...
Figure 1 illustrates the alignment result when one protein sequence and one DNA sequence was aligned using normal protein-DNA alignment algorithm. The frame used was frame 1 for the DNA sequence. As shown in the picture, there was a gap of 2 amino acids (6 nucleic acids) in the alignment, which results the total low score of -2.
This page is a subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general understanding of large-scale DNA or protein alignments; Visualize alignments for figures and publication; Manually edit and curate automatically generated alignments; Analysis in depth
Alignment of cDNA sequences to a genome. Nucleotide DECIPHER: Alignment of rearranged genomes using 6 frame translation: Nucleotide FLAK Fuzzy whole genome alignment and analysis: Nucleotide GMAP Alignment of cDNA sequences to a genome. Identifies splice site junctions with high accuracy. Nucleotide Splign Alignment of cDNA sequences to a genome.
Fast statistical alignment or FSA is a multiple sequence alignment program for aligning many proteins, RNAs, or long genomic DNA sequences. Along with MUSCLE and MAFFT, FSA is one of the few sequence alignment programs which can align datasets of hundreds or thousands of sequences. FSA uses a different optimization criterion which allows it to ...