Difference between revisions of "Scoring Matrix"

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(Created page with '[[MatrixView if the Blosum 62 scoring matix]] [[MatrixView of a c...')
 
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[[Image:MatrixView-blosum62.png|thumb|right|500px|[[MatrixView]] if the Blosum 62 scoring matix]]
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[[Image:MatrixView-blosum62.png|thumb|right|500px|[[MatrixView]] of the Blosum 62 scoring matix]]
  
 
[[Image:MatrixView-vertebrate-codon.png|thumb|right|500px|[[MatrixView]] of a codon scoring matrix generated from vertebrate genome alignments]]
 
[[Image:MatrixView-vertebrate-codon.png|thumb|right|500px|[[MatrixView]] of a codon scoring matrix generated from vertebrate genome alignments]]
  
 
Scoring matrices are used to determine the relative score made by matching two characters in a sequence alignment.  These are usually log-odds of the likelihood of two characters being derived from a common ancestral character.  There are many flavors of scoring matrices for amino acid sequences, nucleotide sequences, and codon sequences, and each is derived from the alignment of "known" [[homologous]] sequences.  These alignments are then used to determine the likelihood of one character being at the same position in the sequence as another character.
 
Scoring matrices are used to determine the relative score made by matching two characters in a sequence alignment.  These are usually log-odds of the likelihood of two characters being derived from a common ancestral character.  There are many flavors of scoring matrices for amino acid sequences, nucleotide sequences, and codon sequences, and each is derived from the alignment of "known" [[homologous]] sequences.  These alignments are then used to determine the likelihood of one character being at the same position in the sequence as another character.

Revision as of 21:42, 21 February 2010

MatrixView of the Blosum 62 scoring matix
MatrixView of a codon scoring matrix generated from vertebrate genome alignments

Scoring matrices are used to determine the relative score made by matching two characters in a sequence alignment. These are usually log-odds of the likelihood of two characters being derived from a common ancestral character. There are many flavors of scoring matrices for amino acid sequences, nucleotide sequences, and codon sequences, and each is derived from the alignment of "known" homologous sequences. These alignments are then used to determine the likelihood of one character being at the same position in the sequence as another character.