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US 11,456,057 B2Granted
Biological sequence distance explorer system providing user visualization of genomic distance between a set of genomes in a dynamic zoomable fashion
AssigneeInternational Business Machines Corporation
InventorsMatthew Davis, James Kaufman, Mark Kunitomi
Life of this patent
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Abstract
One embodiment provides for a method including determining, by at least one processor, sequence-sequence distances for a biological sequence collection. The at least one processor generates a matrix Mij of the sequence-sequence distances, where i and j are positive integers. The at least one processor further generates clusters for the matrix Mij by performing hierarchical clustering. A self-consistent taxonomy is created from the clusters. A visual heat map display of the matrix Mij is selectively controlled using metadata, zoom input and opacity input.
Claims20
A method comprising:
- generating, by an at least one processor, a matrix based on a plurality of sequence-sequence distances for a biological sequence collection;
- generating, by the at least one processor, clusters by performing hierarchical clustering on the matrix;
- creating a taxonomic tree based on the clusters;
- sorting elements of the matrix based on an order of leaf nodes of the taxonomic tree;
- rendering the matrix with the sorted elements as a visual heat map;
- displaying a visualization comprising the visual heat map and the taxonomic tree, wherein the taxonomic tree dynamically scans and zooms with the visual heat map;
- and verifying polymerase chain reaction (PCR) primer design of a PCR primer by:
- receiving, as input, a provided sequence that the PCR primer is built on, wherein the provided sequence is designed to hit a target sequence of DNA from a target group of organisms;
- generating a first overlay highlighting one or more portions of the visual heat map, wherein the one or more portions highlighted by the first overlay include all genomes that contain the provided sequence;
- identifying false negative test results by generating a second overlay highlighting one or more portions of the first overlay, wherein the second overlay includes genomes within the target sequence of DNA from the target group that are not included in the provided sequence;
- identifying false positive test results by generating a third overlay highlighting one or more other portions of the first overlay, wherein the third overlay include genomes outside of the target sequence of DNA from the target group, and wherein the first overlay, the second overlay, and the third overlay have different colors;
- measuring false positive rates based on the false positive test results identified;
- and
- determining specificity of the PCR primer based on the false positive rates.
11 more elements
A non-transitory computer program product comprising a computer readable storage medium having program instructions embodied therewith, the program instructions configured so as to be executable by at least one processor to cause the at least one processor to:
- determine, by the at least one processor, a plurality of sequence-sequence distances for a biological sequence collection;
- generate, by the at least one processor, a matrix based on the plurality of sequence-sequence distances;
- generate, by the at least one processor, clusters by performing hierarchical clustering on the matrix;
- create, by the at least one processor, a taxonomic tree based on the clusters;
- sort elements of the matrix based on an order of leaf nodes of the taxonomic tree;
- render the matrix with the sorted elements as a visual heat map;
- display, by the at least one processor, a visualization comprising the visual heat map and the taxonomic tree, wherein the taxonomic tree dynamically scans and zooms with the visual heat map;
- and
- verify, by the at least one processor, polymerase chain reaction (PCR) primer design of a PCR primer by:
- receiving, as input, a provided sequence that the PCR primer is built on, wherein the provided sequence is designed to hit a target sequence of DNA from a target group of organisms;
- generating a first overlay highlighting one or more portions of the visual heat map, wherein the one or more portions highlighted by the first overlay include all genomes that contain the provided sequence;
- identifying false negative test results by generating a second overlay highlighting one or more portions of the first overlay, wherein the second overlay include genomes within the target sequence of DNA from the target group that are not included in the provided sequence;
- identifying false positive test results by generating a third overlay highlighting one or more other portions of the first overlay, wherein the third overlay include genomes outside of the target sequence of DNA from the target group, and wherein the first overlay, the second overlay, and the third overlay have different colors;
- measuring false positive rates based on the false positive test results identified;
- and
- determining specificity of the PCR primer based on the false positive rates.
13 more elements
A system comprising:
- a memory storing instructions;
- and
- at least one processor that executes the instructions to perform a process comprising:
- determining a plurality of sequence-sequence distances for a biological sequence collection;
- generating a matrix based on the plurality of sequence-sequence distances;
- generating clusters by performing hierarchical clustering on the matrix;
- creating a taxonomic tree based on the clusters;
- sorting elements of the matrix based on an order of leaf nodes of the taxonomic tree;
- rendering the matrix with the sorted elements as a visual heat map;
- displaying a visualization comprising the visual heat map and the taxonomic tree, wherein the taxonomic tree dynamically scans and zooms with the visual heat map;
- and
- verifying polymerase chain reaction (PCR) primer design of a PCR primer by:
- receiving, as input, a provided sequence that the PCR primer is built on, wherein the provided sequence is designed to hit a target sequence of DNA from a target group of organisms;
- generating a first overlay highlighting one or more portions of the visual heat map, wherein the one or more portions highlighted by the first overlay include all genomes that contain the provided sequence;
- identifying false negative test results by generating a second overlay highlighting one or more portions of the first overlay, wherein the second overlay include genomes within the target sequence of DNA from the target group that are not included in the provided sequence;
- identifying false positive test results by generating a third overlay highlighting one or more other portions of the first overlay, wherein the third overlay include genomes outside of the target sequence of DNA from the target group, and wherein the first overlay, the second overlay, and the third overlay have different colors;
- measuring false positive rates based on the false positive test results identified;
- and
- determining specificity of the PCR primer based on the false positive rates.
16 more elements
Dependencies are inferred from the claim text.