Global 和Local以及Pairwise与MSA序列比对的
2019-02-07 本文已影响18人
爱折腾的大懒猪
Difference between Global and Local Alignment
下面的表格很好地总结了Global和Local比对的差异, 对于一般只是使用的人, 只要记住, Global适用于功能相似序列(例如同源序列比对)的比对, 而Local适用于查找子序列, 就是局部相似性很高的序列. 后者尤其常用语BLAST. Global使用的是著名的"针人"算法, Local使用的是著名的"水人"算法.
## Local Alignment
5' ACTACTAGATTACTTACGGATCAGGTACTTTAGAGGCTTGCAACCA 3'
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5' TACTCACGGATGAGGTACTTTAGAGGC 3'
## Global Alignment
5' ACTACTAGATTACTTACGGATCAGGTACTTTAGAGGCTTGCAACCA 3'
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5' ACTACTAGATT----ACGGATC--GTACTTTAGAGGCTAGCAACCA 3'
Difference between Global and Local Alignment
| Global Sequence Alignment | Local Sequence Alignment |
|---|---|
| In global alignment, an attempt is made to align the entire sequence (end to end alignment) | Finds local regions with the highest level of similarity between the two sequences. |
| A global alignment contains all letters from both the query and target sequences | A local alignment aligns a substring of the query sequence to a substring of the target sequence. |
| If two sequences have approximately the same length and are quite similar, they are suitable for global alignment. | Any two sequences can be locally aligned as local alignment finds stretches of sequences with high level of matches without considering the alignment of rest of the sequence regions. |
| Suitable for aligning two closely related sequences. | Suitable for aligning more divergent sequences or distantly related sequences. |
| Global alignments are usually done for comparing homologous genes like comparing two genes with same function (in human vs. mouse) or comparing two proteins with similar function. | Used for finding out conserved patterns in DNA sequences or conserved domains or motifs in two proteins. |
| A general global alignment technique is the Needleman–Wunsch algorithm. | A general local alignment method is Smith–Waterman algorithm. |
| Examples of Global alignment tools: (1) EMBOSS Needle (2) Needleman-Wunsch Global Align Nucleotide Sequences (Specialized BLAST) | Examples of Local alignment tools: (1) BLAST; (2) EMBOSS Water (3) LALIGN |
全局比对使用 Needleman–Wunsch算法, 而局部比对使用Smith–Waterman algorithm
Difference between Pairwise and Multiple Sequence Alignment
Pairwise是以两条序列为基础进行比对, 适合相似性搜索, 典型的如BLAST, Needle, Water等. MSA是以多条序列同时进行考虑和比较, 使用更复杂的算法进行处理, 而非简单的两两比对. 主要用途时找寻一个家族蛋白的保守域和多变域, 也可以用于考察序列间进化关系等.
Difference between Pairwise and Multiple Sequence Alignment
| Pairwise Alignment | Multiple Sequence Alignment (MSA) |
|---|---|
| An alignment procedure comparing two biological sequences of either protein, DNA or RNA | An alignment procedure comparing three or more biological sequences of either protein, DNA or RNA |
| Pairwise alignments can be generally categorized as global or local alignment methods. | MSA is generally a global multiple sequence alignment |
| Comparatively simple algorithm is used | Complex sophisticated algorithm is used |
| A general global alignment technique is the Needleman–Wunsch algorithm. A general local alignment method is Smith–Waterman algorithm. | A technique called progressive alignment method is employed. In this approach, a pairwise alignment algorithm is used iteratively, first to align the most closely related pair of sequences, then the next most similar one to that pair, and so on. |
| Applications: a) Primarily to find out conserved regions between the two sequences. b)Similarity searches in a database | Applications: a) To detect regions of variability or conservation in a family of proteins; b) Phylogenetic analysis (inferring a tree, estimating rates of substitution, etc.) ; c) Detection of homology between a newly sequenced gene and an existing gene family prediction of protein structure; d) Demonstration of homology in multigene families |
| Examples of pairwise alignment tools: LALIGN, BLAST, EMBOSS Needle; EMBOSS Water | Examples of Multiple Sequence Alignment tools: MUSCLE; T-Coffee; MAFFT; CLUSTALW |
