Window-based method for determining inherited segments
Displaying a comparison of genetic data is disclosed, including receiving an indication of a first individual, receiving an indication of a second individual, retrieving the genotypic information for the first individual and the second individual, comparing the genotypic information of the first individual and the second individual, displaying an indication of the comparison of the genotypic information of the first individual and the second individual graphically. A first graphical symbol is used to display an indication of the genome regions for which the first individual and the second individual are identical. A second graphical symbol is used to display an indication of the genome regions for which the first individual and the second individual are half identical.
1. A computer-implemented method comprising
receiving, by one or more processors and by way of a graphical user interface, a selection of at least one of a first individual and a second individual, wherein the selection is made either through a menu or text entry;
retrieving, by the one or more processors and from a database, representations of diploid sequences of the first individual and the second individual, wherein the diploid sequences include values for markers;
comparing, by the one or more processors, the representations of diploid sequences of the first individual and the second individual using windows of a fixed size;
identifying, by the one or more processors as identical segments, the windows for which the values of markers on both of the diploid sequences are identical for the first individual and the second individual;
identifying, by the one or more processors as half-identical segments, the windows for which the values of markers on only one of the diploid sequences are identical for the first individual and the second individual;
identifying, by the one or more processors as non-identical segments, the windows for which the markers on neither of the diploid sequences are identical for the first individual and the second individual; and
providing for display, by the one or more processors and on the graphical user interface, a visual indication of the diploid sequences wherein: the diploid sequences are displayed in order of their numbering, a first color, shading, or fill pattern is used to depict locations of the identical segments, a second color, shading, or fill pattern is used to depict locations of the half-identical segments, and a third color, shading, or fill pattern is used to depict the non-identical segments.
2. The computer-implemented method of claim 1 , further comprising:
receiving, by the one or more processors, a type of the diploid sequences, wherein the visual indication includes a subset of the diploid sequences that are related to the type.
3. The computer-implemented method of claim 2 , wherein the type comprises a particular trait or a particular location within the diploid sequences.
4. The computer-implemented method of claim 2 , wherein the type is a one of traits relating to bitter tasting, circadian rhythm, endurance, female fertility, immune system compatibility, non-bitter tasting, pigmentation, or weight body mass index.
5. The computer-implemented method of claim 2 , wherein the type comprises a user-specified type of genotypic information.
6. The computer-implemented method of claim 1 , further comprising:
receiving, by the one or more processors, an indication that the comparison is a whole genome comparison, wherein the visual indication includes all of the diploid sequences for a given genome.
7. The computer-implemented method of claim 1 , wherein a common shape is used to depict locations of the identical segments, the half-identical segments, and the non-identical segments.
8. The computer-implemented method of claim 1 , wherein different shapes used to depict locations of the identical segments, the half-identical segments, and the non-identical segments.
9. The computer-implemented method of claim 1 , wherein a fourth color, shading, or fill pattern is used to depict segments that do not contain enough markers to determine whether they are identical, half-identical, or non-identical.
10. The computer-implemented method of claim 1 , wherein the visual indication of the diploid sequences for the identical segments, the half-identical segments, and the non-identical segments include separate indications for each chromosome in the diploid sequences.
11. The computer-implemented method of claim 1 , wherein the windows of the fixed size are 10 Centimorgans in length.
12. A non-transitory computer readable storage medium comprising computer instructions that, when executed by one or more processors, cause a computing system to perform operations comprising:
receiving, by way of a graphical user interface, a selection of at least one of a first individual and a second individual, wherein the selection is made either through a menu or text entry;
retrieving, from a database, representations of diploid sequences of the first individual and the second individual, wherein the diploid sequences include values for markers;
comparing the representations of diploid sequences of the first individual and the second individual using windows of a fixed size;
identifying, as identical segments, the windows for which the values of markers on both of the diploid sequences are identical for the first individual and the second individual;
identifying, as half-identical segments, the windows for which the values of markers on only one of the diploid sequences are identical for the first individual and the second individual;
identifying, as non-identical segments, the windows for which the markers on neither of the diploid sequences are identical for the first individual and the second individual; and
providing for display, on the graphical user interface, a visual indication of the diploid sequences wherein: the diploid sequences are displayed in order of their numbering, a first color, shading, or fill pattern is used to depict locations of the identical segments, a second color, shading, or fill pattern is used to depict locations of the half-identical segments, and a third color, shading, or fill pattern is used to depict the non-identical segments.
13. The non-transitory computer readable storage medium of claim 12 , the operations further comprising:
receiving a type of the diploid sequences, wherein the visual indication includes a subset of the diploid sequences that are related to the type.
14. The non-transitory computer readable storage medium of claim 13 , wherein the type comprises a particular trait or a particular location within the diploid sequences.
15. The non-transitory computer readable storage medium of claim 13 , wherein the type is a one of traits relating to bitter tasting, circadian rhythm, endurance, female fertility, immune system compatibility, non-bitter tasting, pigmentation, or weight body mass index.
16. The non-transitory computer readable storage medium of claim 12 , wherein a common shape is used to depict locations of the identical segments, the half-identical segments, and the non-identical segments.
17. The non-transitory computer readable storage medium of claim 12 , wherein different shapes used to depict locations of the identical segments, the half-identical segments, and the non-identical segments.
18. The non-transitory computer readable storage medium of claim 12 , wherein a fourth color, shading, or fill pattern is used to depict segments that do not contain enough markers to determine whether they are identical, half-identical, or non-identical.
19. The non-transitory computer readable storage medium of claim 12 , wherein the visual indication of the diploid sequences for the identical segments, the half-identical segments, and the non-identical segments include separate indications for each chromosome in the diploid sequences.
20. A computing system comprising:
one or more processors;
memory; and
program instructions, stored in the memory, that upon execution by the one or more processors cause the computing system to perform operations comprising:
receiving, by way of a graphical user interface, a selection of at least one of a first individual and a second individual, wherein the selection is made either through a menu or text entry;
retrieving, from a database, representations of diploid sequences of the first individual and the second individual, wherein the diploid sequences include values for markers;
comparing the representations of diploid sequences of the first individual and the second individual using windows of a fixed size;
identifying, as identical segments, the windows for which the values of markers on both of the diploid sequences are identical for the first individual and the second individual;
identifying, as half-identical segments, the windows for which the values of markers on only one of the diploid sequences are identical for the first individual and the second individual;
identifying, as non-identical segments, the windows for which the markers on neither of the diploid sequences are identical for the first individual and the second individual; and
providing for display, on the graphical user interface, a visual indication of the diploid sequences wherein: the diploid sequences are displayed in order of their numbering, a first color, shading, or fill pattern is used to depict locations of the identical segments, a second color, shading, or fill pattern is used to depict locations of the half-identical segments, and a third color, shading, or fill pattern is used to depict the non-identical segments.