Statistical methods for analyzing biological sequences
AssigneeBoard of Regents, The University of Texas System
InventorsRama Ranganathan, Steve Lockless
Life of this patent
Estimating the term…
Abstract
Statistical algorithms that are useful to aid in the identification of evolutionarily conserved amino acid positions within a family of proteins, and in the identification of interacting amino acid positions within a protein sequence are disclosed. The algorithms may also be useful in the analysis of other polymer sequences such as polysaccharides, lipids, deoxyribonucleic acid (DNA), and ribonucleic acid sequences (RNA), and, more specifically, in the analysis of DNA microarray data. Algorithms useful for analyzing the structural changes of perturbations to determine the mechanisms by which positions are coupled are also disclosed.
Claims20
1-34. (canceled)
A method of identifying one or more nucleic acid positions in a group of nucleic acid sequences, the method comprising:
- (a) accessing data representing a multiple sequence alignment (MSA) of a plurality of nucleic acid sequences;
- and
- (b) identifying one or more evolutionarily conserved nucleic acid positions within the MSA using the following equation:
- Δ
-
-
- G
- i
- stat
- =
- kT
- *
-
- ∑
- x
-
- (
- ln
-
- P
- i
- x
- P
- MSA
- x
- )
- 2
- wherein:
- i is a position in the MSA;
- ΔGistat is the conservation energy value for position i;
- Pix is the probability of nucleic acid x at position i;
- PMSAx is the probability of nucleic acid x in the MSA;
- and
- kT* is an energy unit, where k is Boltzmann's constant.
A method of identifying one or more nucleic acid positions in a group of nucleic acid sequences, the method comprising:
- (a) accessing data representing a multiple sequence alignment (MSA) of a plurality of nucleic acid sequences;
- (b) calculating a conservation energy value for each position in the MSA using the following equation:
- Δ
-
-
- G
- i
- stat
- =
- kT
- *
-
- ∑
- x
-
- (
- ln
-
- P
- i
- x
- P
- MSA
- x
- )
- 2
- wherein:
- i is a position in the MSA;
- ΔGistat is the conservation energy value for position i;
- Pix is the probability of nucleic acid x at position i;
- PMSAx is the probability of nucleic acid x in the MSA;
- kT* is an energy unit, where k is Boltzmann's constant;
- and
- (c) identifying one or more positions within the MSA that have statistically significant conservation energy values.
A method of calculating conservation energy values for amino acids in an alignment of protein sequences, the method comprising:
- (a) accessing data representing a multiple sequence alignment (MSA) of a plurality of protein sequences;
- and
- (b) calculating a conservation energy value, ΔGistat, for each of multiple amino acids in the MSA at a given position i in the MSA using the following equation:
- Δ
-
-
- G
- i
- stat
- =
- kT
- *
-
- ∑
- x
-
- (
- ln
-
- P
- i
- x
- P
- MSA
- x
- )
- 2
- where:
- Pix is the probability of amino acid x at position i;
- PMSAx is the probability of amino acid x in the MSA;
- and
- kT* is an energy unit, where k is Boltzmann's constant.
A method of calculating conservation energy values for nucleic acids in an alignment of nucleic acid sequences, the method comprising:
- (a) accessing data representing a multiple sequence alignment (MSA) of a plurality of nucleic acid sequences;
- and
- (b) calculating a conservation energy value, ΔGistat, for each of multiple nucleic acids in the MSA at a given position i in the MSA using the following equation:
- Δ
-
-
- G
- i
- stat
- =
- kT
- *
-
- ∑
- x
-
- (
- ln
-
-
- P
- i
- x
- P
- MSA
- x
- )
- 2
- where:
- Pix is the probability of nucleic acid x at position i;
- PMSAx is the probability of nucleic acid x in the MSA;
- and
- kT* is an energy unit, where k is Boltzmann's constant.
Dependencies are inferred from the claim text.