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US 7,734,421 B2Granted
Method for identifying motifs and/or combinations of motifs having a boolean state of predetermined mutation in a set of sequences and its applications
AssigneeCentre National de la Recherche Scientifique (CNRS)
InventorsAnne Vanet, Michaela Muller-Trutwin, Thomas Valere
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Abstract
A method for identifying a motif or a combination of motifs having a Boolean state of predetermined mutations in a set of sequences including a) aligning a set of sequences of ordered motifs represented by a single-character code, b) comparing a reference sequence with the set of sequences aligned in step (a), c) identifying motifs not having mutated simultaneously or motifs having mutated simultaneously at least once on at least one sequence of the set and not having mutated on another sequence of the set.
Claims14
A method for identifying a motif or a combination of motifs having a Boolean state of predetermined mutations in a set of sequences comprising:
- a) aligning a set of sequences of ordered motifs represented by a single-character code on a programmed computer using a multiple sequence alignment program,
- b) comparing a reference sequence with the set of sequences aligned in step (a) by forming a first numerical matrix A of dimensions N×M in which N designates a number of sequences and M designates a number of motifs of one sequence of said alignment, with value Ai,j being equal to a first value A1 when the motif of position i of sequence j with a value ranging from 0 to N is mutated in relation to a motif of position i of the reference sequence and equal to a second value A2 in other cases,
- forming two analysis matrices B and C of mutations in which:
- matrix B is a matrix of unmutated couples, of couples which do not mutate simultaneously, of dimension M×M, value Bi,k=Bk,i being equal:
- to a first value B1 when Ai,j=Ak,j=A1 irrespective of the value of j ranging from 0 to N,
- to a second value B2 in other cases;
- matrix C is a matrix of mutated couples of dimension M×M, value Ck,i=Ci,k being equal:
- to a second value C1 when Ai,j=Ak,j irrespective, of the value of j ranging from 0 to N,
- to a first value C2 in other cases;
- determining for a set E of positions a coefficient RE whose value is R1 when values Bi,k are equal to a second value B2, irrespective of the values of i and k belonging to set E of said positions,
- determining for a set F of positions, a coefficient RF, the value of which is R1 when values Ci,k are equal to second value C2, irrespective of the values of i and k belonging to set F of said positions;
- wherein in the matrices, i and k designate positions and j designates a sequence, and
- c) identifying motifs not having mutated simultaneously or motifs having mutated simultaneously at least once on at least one sequence of the set and not having mutated on another sequence of said set.
10 more elements
A method for identifying a motif or a combination of motifs having a Boolean state of predetermined mutations in a set of sequences comprising:
- a) aligning a set of sequences of ordered motifs represented by a single-character code on a programmed computer using a CLUSTAL algorithm based multiple sequence alignment program or a Hidden Markov Model algorithm based multiple sequence alignment program,
- b) comparing a reference sequence with the set of sequences aligned in step (a) by forming a first numerical matrix A of dimensions N×M in which N designates a number of sequences and M designates a number of motifs of one sequence of said alignment, with value Ai,j being equal to a first value A1 when the motif of position i of sequence j with a value ranging from 0 to N is mutated in relation to a motif of position i of the reference sequence and equal to a second value A2 in other cases,
- forming two analysis matrices B and C of mutations in which:
- matrix B is a matrix of unmutated couples, of couples which do not mutate simultaneously, of dimension M×M, value Bi,k=Bk,i being equal:
- to a first value B1 when Ai,j=Ak,j irrespective of the value of j ranging from 0 to N,
- to a second value B2 in other cases;
- matrix C is a matrix of mutated couples of dimension M×M, value Ck,i=Cj,k being equal:
- to a second value C1 when Ai,j=Ak,j irrespective of the value of j ranging from 0 to N,
- to a first value C2 in other cases;
- determining for a set E of positions a coefficient RE whose value is R1 when values Bi,k are equal to a second value B2, irrespective of the values of i and k belonging to set E of said positions,
- determining for a set F of positions, a coefficient RF, the value of which is R1 when values Ci,k are equal to second value C2, irrespective of the values of i and k belonging to set F of said positions;
- wherein in the matrices, i and k designate positions and j designates a sequence, and
- c) identifying motifs not having mutated simultaneously or motifs having mutated simultaneously at least once on at least one sequence of the set and not having mutated on another sequence of said set.
10 more elements
Dependencies are inferred from the claim text.