An Introduction to Sequence Similarity (“Homology”) Searching
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Cites background from "An Introduction to Sequence Similar..."
...Unfortunately, MSA methods tend to vary significantly, and there is currently no quantitative measure for the quality of alignment (Nuin et al., 2006; Kemena and Notredame, 2009; Pearson, 2013)....
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...Difficulties arise with MSAs containing sequences of varying length, or when there are clusters of sequences that are locally, but not globally, homologous (Rost, 1999; Pearson, 2013)....
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References
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"An Introduction to Sequence Similar..." refers methods in this paper
...More recent multiple sequence alignment methods, like MAFFT (Katoh et al., 2002) and MUSCLE (Edgar, 2004), use iterative approaches that allow gaps to be re-positioned....
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...MUSCLE: Multiple sequence alignment with high accuracy and high throughput....
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25,325 citations
"An Introduction to Sequence Similar..." refers methods in this paper
...During the 1980s, progressive alignment strategies, like ClustalW (Larkin et al., 2007; UNIT 2.3) were developed that simplified the problem to O(n2l2), where n is the number of sequences, and l is their average length....
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12,432 citations
"An Introduction to Sequence Similar..." refers background in this paper
...Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the smith-waterman and FASTA algorithms....
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...BLAST, FASTA, SSEARCH, and other commonly used similarity searching programs produce accurate statistical estimates that can be used to reliably infer homology....
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...However, the probability p(b) is not what is reported by BLAST, FASTA, or SSEARCH, because it reflects the probability of the score in a single pairwise alignment....
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...BLAST, SSEARCH, FASTA, and HMMER calculate local sequence alignments; local alignments identify the most similar region between two sequences....
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...Homology (common ancestry and similar structure) can be reliably inferred from statistically significant similarity in a BLAST, FASTA, SSEARCH, or HMMER search, but to infer that two proteins are homologous does not guarantee that every part of one protein has a homolog in the other....
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12,003 citations
"An Introduction to Sequence Similar..." refers methods in this paper
...More recent multiple sequence alignment methods, like MAFFT (Katoh et al., 2002) and MUSCLE (Edgar, 2004), use iterative approaches that allow gaps to be re-positioned....
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...MAFFT: A novel method for rapid multiple sequence alignment based on fast fourier transform....
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