Using a smaller word size (Minimal Size of Exact Match) will increase the computational time.

Using a larger mismatch number (Number of Mismatch in the Word) will increase the computational time.

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What it does

This tool currently uses the BLAT alignment program. Your short reads file is searched against a genome build or another uploaded file.

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Example

• Input a multiple fasta file:

  >seq1
  TGGTAATGGTGGTTTTTTTTTTTTTTTTTTATTTTT
  

• Use the default settings:

  • alignment identity must be higher than or equal to 90%.
  • minimal size of exact match to trigger an alignment is 11.
  • allow 0 mismatches in the above exact match size.

• Search against ce2 (C. elegans March 2004), partial result:

  25 1 0 0 0 0 0 0 + seq1 36 10 36 chrI 15080483 9704438 9704464 1 26, 10, 9704438, ggttttttttttttttttttattttt, ggtttttttttttttttttttttttt,
  27 0 0 0 0 0 1 32 + seq1 36 9 36 chrI 15080483 1302536 1302595 2 21,6, 9,30, 1302536,1302589, tggtttttttttttttttttt,attttt, tggtttttttttttttttttt,attttt,
  

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Parameters

• Minimal Identity (-minIdentity) : In percent, the minimum sequence identity between the query and target alignment. Default is 90.
• Minimal Size of Exact Match (-tileSize) : The size of a match that will trigger an alignment. Default is 11. Usually between 8 and 12. Must be between 6 and 18.
• Number of Mismatch in the Word (-oneOff) : The number of mismatches allowed in the word (tile size) and still triggers an alignment. Default is 0.

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Reference

BLAT: Kent, W James, BLAT--the BLAST-like alignment tool. (2002) Genome Research:12(4) 656-664.