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Sequence Similarity Searching

A guide to sequence similarity searching using BLAST and other tools.

Background

Sequence similarity searches can be done in multiple ways on multiple platforms.  BLAST (Basic Local Alignment Search Tool) aligns a sequence to a database of other sequences or can align two sequences to each other.  BLAST can be done with nucleotide sequences or with amino acid protein sequences.  There are a number of special BLAST variations that allow searching among more dissimilar sequences.  Multiple sequence alignment (done by CLUSTAL, COBALT, MUSCLE, ProbCons and others) consists of aligning several sequences to each other.

Why use BLAST?

Specialized BLAST tools are available for many purposes; choosing the right BLAST tool and utilizing it properly can help you:

  • Find statistically significant matches, based on sequence similarity, to a protein or nucleotide sequence of interest
  • Obtain information on the inferred function of a gene or protein
  • Help determine whether an implied homology between two sequences is justified
  • Find conserved domains in your sequence that are common to many sequences 
  • Search for sequence motifs or patterns that are similar to a sequence of interest in a particular region 
  • Compare known sequences from different taxonomic groups 
  • Limit a search to particular segments of the database such as a particular species' genome
  • Search for a protein sequence of interest using a nucleotide sequence as the query and vice versa
  • Discover suspected cloning vector sequences in your sequence