7 Difference Between Global And Local Sequence Alignment

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What Is Sequence Alignment?

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. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in financial data.

Global Sequence Alignment

Global alignment is used to compare sequences in cases where we have reason to believe that the sequences are related along their entire length. If for example, sequences s and t are two independent sequencing runs of the same PCR product, then they should differ only in positions where there are sequencing errors. In order to find those sequencing errors, we align all of sequence s with all of sequence t. Other applications of global alignment include finding mutations in closely related gene or protein sequences and identification of single nucleotide polymorphisms (SNPs).

Examples of Global alignment tools include:

  • EMBOSS Needle
  • Needleman-Wunsch Global Align Nucleotide Sequences (Specialized BLAST)

What You Need To Know About Local Sequence Alignment

  • In global alignment, an attempt is made to align the entire sequence (end to end alignment).
  • A global alignment contains all letters from both the query and target sequences.
  • If two sequences have approximately the same length and are quite similar, they are suitable for global alignment.
  • Suitable for aligning two closely 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.
  • A general global alignment technique is the Needleman–Wunsch algorithm.

Local Sequence Alignment

Local alignment addresses cases where we only expect to find isolated regions of similarity. One example is alignment of genomic DNA upstream from two co-expressed genes to find conserved regions that may correspond to transcription factor binding sites. Another application is identification of conserved domains1 in two amino acid sequences that encode proteins that share one or more domains, but are otherwise unrelated.

Examples of Local alignment tools include:

  • BLAST
  • EMBOSS Water
  • LALIGN

What You Need To Know About Local Sequence Alignment

  • Finds local regions with the highest level of similarity between the two sequences.
  • A local alignment aligns a substring of the query sequence to a substring of the target sequence.
  • 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 more divergent sequences or distantly related sequences.
  • Used for finding out conserved patterns in DNA sequences or conserved domains or motifs in two proteins.
  • A general local alignment method is Smith–Waterman algorithm.

Also Read: Difference Between Replication And Transcription

Difference Between Global And Local Sequence Alignment In Tabular Form

BASIS OF COMPARISON GLOBAL SEQUENCE ALIGNMENT LOCAL SEQUENCE ALIGNMENT
Description 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.  
Examples Of Tools -EMBOSS Needle    

-Needleman-Wunsch Global Align Nucleotide Sequences (Specialized BLAST)  
-BLAST
 
-EMBOSS Water
 
-LALIGN  
Function 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.  
Two Sequences 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.  
Suitability Suitable for aligning two closely related sequences.   Suitable for aligning more divergent sequences or distantly related sequences.  
Use 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.  
General Technique A general global alignment technique is the Needleman–Wunsch algorithm.   A general local alignment method is Smith–Waterman algorithm.  

Also Read: Difference Between Pairwise And Multiple Sequence Alignment

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