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Compare Two Sequence To Find The Maximum Similarity

We know BLAST can compare two sequences, however it compares sequences by lining up them. My question is can we shift one sequence then compare the other. Let me give you a simple example:the length is 15

GTTCCTAGTCTAGAC
TCCTAGTCTAGACTT

If we shift it and compare

GTTCCTAGTCTAGAC
  |||||||||||||
  TCCTAGTCTAGACTT

Then there are 11 letters hit, we define the score by 11/15=73%. Of course, we can shift to whatever we want. How to find the max score? Is there such a software to do it? Thanks.

sequence blast
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updated by Woa Woa • written by Love • Love

With the above example, you are talking about sequence identity not similarity.

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written by Larry_Parnell Larry_Parnell

Istvan is correct - strictly speaking BLAST does not compare two sequences. It is possible to align two sequences with BLAST - see Bl2Seq at http://blast.ncbi.nlm.nih.gov/Blast.cgi. Nonetheless, BLOAST is not a reliable tool for the goal you have in mind.

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written by Larry_Parnell Larry_Parnell

2 answers

what about using a simple Smith & Waterman algorithm ? e.g: emboss water

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written by Pierre Lindenbaum Pierre Lindenbaum

This is exactly how I would approach this.

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written by Larry_Parnell Larry_Parnell

I think that the goal is to propose a method, not to use an available one.

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written by Manu Prestat Manu Prestat

OK, so run SW iteratively shifting the query or alignment to the n+1 position with each successive comparison. There, method and tool are now together.

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written by Larry_Parnell Larry_Parnell

Matching by shifting can't handle internal gaps(Indels), they can put gaps only at the extremities of the sequences

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written by Woa Woa

neither substitution, sequencing errors, homology...

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written by Manu Prestat Manu Prestat

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