Systems, methods, and computer program products for merging a new nucleotide or amino acid sequence into operational taxonomic units
AssigneeUniversity of Guelph
InventorsPaul Hebert, Sujeevan Ratnasingham
Life of this patent
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Abstract
The present disclosure provides a method for filtering sequence clusters during a process of merging a newly generated nucleotide or amino acid sequence with a set of previously clustered sequences. In another aspect, the disclosure provides a method for assigning newly generated nucleotide or amino acid sequences to presumptive species called operational taxonomic units. In yet another embodiment, the sequences are derived from the cytochrome c oxidase I gene.
Claims19
A method for operating a computer system to filter out clusters from a group of clusters from further consideration during a process of merging a new nucleic acid or amino acid sequence into the group of clusters based on sequence similarity, the computer comprising a processor and a memory, the method comprising:
- a) determining a candidate cluster set including a plurality of candidate clusters, each candidate cluster comprising a plurality of previously classified nucleic acid or amino acid sequences wherein each previously classified nucleic acid or amino acid sequence in a cluster is closer to at least one other previously classified nucleic acid or amino acid sequence in that cluster than to any previously classified nucleic acid or amino acid sequences in other clusters;
- b) using the processor of the computer system to determine a plurality of sets of representative sequences, by determining, for each of the candidate clusters in the candidate cluster set, a set of one or more representative sequences, wherein for at least one candidate cluster, the number of representative sequences in the set of one or more representative sequences of the candidate cluster is less than the number of previously classified nucleic acid or amino acid sequences in the plurality of previously classified nucleic acid or amino acid sequences of the candidate cluster;
- c) using the processor to determine a plurality of candidate cluster distance measures, by determining, for each of the candidate clusters in the candidate cluster set, a candidate cluster distance measure between the new nucleic acid or amino acid sequence and the candidate cluster, wherein the candidate cluster distance measure between the new nucleic acid or amino acid sequence and the candidate cluster is determined by determining the distance between the nucleic acid or amino acid sequence and the set of one or more representative sequences of the candidate cluster;
- and
- d) using the processor to filter out from further consideration each candidate cluster in the candidate cluster set if and only if the associated candidate cluster distance measure of the candidate cluster is greater than a pre-defined filtering threshold, and retaining and storing in the memory all other candidate clusters in the candidate cluster set for further consideration.
A data processing system for filtering out clusters from a group of clusters from further consideration during a process of merging a new nucleic acid or amino acid sequence into the group of clusters based on sequence similarity, the data processing system comprising a processor, a memory, and instructions recorded in the memory for configuring the processor to
- a) determine a candidate cluster set including a plurality of candidate clusters, each candidate cluster comprising a plurality of previously classified nucleic acid or amino acid sequences wherein each previously classified nucleic acid or amino acid sequence in a cluster is closer to at least one other previously classified nucleic acid or amino acid sequence in that cluster than to any previously classified nucleic acid or amino acid sequences in other clusters;
- b) determine a plurality of sets of representative sequences, by determining, for each of the candidate clusters in the candidate cluster set, a set of one or more representative sequences, wherein for at least one candidate cluster, the number of representative sequences in the set of one or more representative sequences of the candidate cluster is less than the number of previously classified nucleic acid or amino acid sequences in the plurality of previously classified nucleic acid or amino acid sequences of the candidate cluster;
- c) determine a plurality of candidate cluster distance measures, by determining, for each of the candidate clusters in the candidate cluster set, a candidate cluster distance measure between the new nucleic acid or amino acid sequence and the candidate cluster, wherein the candidate cluster distance measure between the new nucleic acid or amino acid sequence and the candidate cluster is determined by determining the distance between the nucleic acid or amino acid sequence and the set of one or more representative sequences of the candidate cluster;
- and
- d) filter out from further consideration each candidate cluster in the candidate cluster set if and only if the associated candidate cluster distance measure of the candidate cluster is greater than a pre-defined filtering threshold, and retaining and storing in the memory all other candidate clusters in the candidate cluster set for further consideration.
(canceled)
A computer program product for use on a computer system to filter out clusters from a group of clusters from further consideration during a process of merging a new nucleic acid or amino acid sequence into the group of clusters based on sequence similarity, the computer program product comprising a non-transitory computer readable recording medium, and instructions recorded on the recording medium for instructing the computer system to
- a) determine a candidate cluster set including a plurality of candidate clusters, each candidate cluster comprising a plurality of previously classified nucleic acid or amino acid sequences wherein each previously classified nucleic acid or amino acid sequence in a cluster is closer to at least one other previously classified nucleic acid or amino acid sequence in that cluster than to any previously classified nucleic acid or amino acid sequences in other clusters;
- b) determine a plurality of sets of representative sequences, by determining, for each of the candidate clusters in the candidate cluster set, a set of one or more representative sequences, wherein for at least one candidate cluster, the number of representative sequences in the set of one or more representative sequences of the candidate cluster is less than the number of previously classified nucleic acid or amino acid sequences in the plurality of previously classified nucleic acid or amino acid sequences of the candidate cluster;
- c) determine a plurality of candidate cluster distance measures, by determining, for each of the candidate clusters in the candidate cluster set, a candidate cluster distance measure between the new nucleic acid or amino acid sequence and the candidate cluster, wherein the candidate cluster distance measure between the new nucleic acid or amino acid sequence and the candidate cluster is determined by determining the distance between the nucleic acid or amino acid sequence and the set of one or more representative sequences of the candidate cluster;
- and
- d) filter out from further consideration each candidate cluster in the candidate cluster set if and only if the associated candidate cluster distance measure of the candidate cluster is greater than a pre-defined filtering threshold, and retaining and storing in the memory all other candidate clusters in the candidate cluster set for further consideration.
(canceled)
A method for operating a computer system to derive data from a plurality of nucleic acid sequences, the computer comprising a processor and a memory, the method comprising:
- providing a plurality of computer-readable sequence representations comprising, for each nucleic acid sequence in the plurality of nucleic acid sequences, a corresponding computer-readable sequence representation having an ordered sequence of residue representations comprising, for each residue in that nucleic acid sequence, a corresponding residue representation, wherein each nucleic acid sequence in the plurality of nucleic acid sequences comprises at least X residues, X being an integer greater than 300;
- providing a scanning window for collecting sequence-specific data for each sequence representation in the plurality of computer-readable sequence representations by sliding along each sequence in the plurality of computer-readable sequence representations, the scanning window having a pre-defined length W defining a number of residue representations in a portion of the sequence representation that are concurrently scannable by the computer by positioning the scanning window over that portion of the sequence representation, W being an integer greater than 10 and less than X;
- operating the processor to position the scanning window at a first portion of the sequence representation, scan the first portion of the sequence representation to obtain first portion scan results;
- and then
- operating the processor to reposition the scanning window at a second portion of the sequence representation, scan the second portion of the sequence representation to obtain second portion scan results, the second portion being different from the first portion.
A data processing system for deriving data from a plurality of nucleic acid sequences, the data processing system comprising a processor, a memory, and instructions recorded in the memory for configuring the processor to
- provide a plurality of computer-readable sequence representations comprising, for each nucleic acid sequence in the plurality of nucleic acid sequences, a corresponding computer-readable sequence representation having an ordered sequence of residue representations comprising, for each residue in that nucleic acid sequence, a corresponding residue representation, wherein each nucleic acid sequence in the plurality of nucleic acid sequences comprises at least X residues, X being an integer greater than 300;
- provide a scanning window for collecting sequence-specific data for each sequence representation in the plurality of computer-readable sequence representations by sliding along each sequence in the plurality of computer-readable sequence representations, the scanning window having a pre-defined length W defining a number of residue representations in a portion of the sequence representation that are concurrently scannable by the computer by positioning the scanning window over that portion of the sequence.
(canceled)
A computer program product for use on a computer system to derive data from a plurality of nucleic acid sequences, the computer program product comprising a non-transitory computer readable recording medium, and instructions recorded on the recording medium for instructing the computer system to
- provide a plurality of computer-readable sequence representations comprising, for each nucleic acid sequence in the plurality of nucleic acid sequences, a corresponding computer-readable sequence representation having an ordered sequence of residue representations comprising, for each residue in that nucleic acid sequence, a corresponding residue representation, wherein each nucleic acid sequence in the plurality of nucleic acid sequences comprises at least X residues, X being an integer greater than 300;
- and
- provide a scanning window for collecting sequence-specific data for each sequence representation in the plurality of computer-readable sequence representations by sliding along each sequence in the plurality of computer-readable sequence representations, the scanning window having a pre-defined length W defining a number of residue representations in a portion of the sequence representation that are concurrently scannable by the computer by positioning the scanning window over that portion of the sequence.
(canceled)
Dependencies are inferred from the claim text.