Genome browser

Abstract

This document describes, among other things, a computer-implemented method for displaying and analyzing sequenced genome data. The method can include obtaining, at a computing system, genomic data for a plurality of organisms. A graphical representation can of the genomic data can be generated by the computing system based at least on the genomic data for the plurality of organisms, and the graphical representation can include a plurality of tracks that are arranged to show one or more features of the genomic data for different ones of the plurality of organisms. The graphical representation can be output for display by the computing system.

1 . A computer-implemented method for displaying and analyzing sequenced genome data, the method comprising:
 generating, by a computing system and based at least on genomic data for the plurality of organisms received by the computing system, a graphical user interface having a graphical representation of the genomic data, the graphical representation comprising:
 a plurality of tracks that are arranged to show one or more features of the genomic data for each organism, wherein the plurality of tracks includes a first track that shows a first particular feature of a first organism, a second track that shows the first particular feature of a second organism, and a third track that shows the first particular feature of a third organism: 
   identifying, by the computing system, that the first organism is designated as a reference organism;   dynamically modifying, by the computing system, the graphical user interface by ordering the plurality of tracks in the graphical representation of the genomic data so that:
 the first track that shows the first particular feature of the first organism is shown in a reference position of the graphical representation, 
 the second and third tracks are shown in respective positions outside of the reference position, and 
 the first particular features of the second and third tracks are each shown 
 relative to the first particular features of the first track. 
   
     
     
         2 . The computer-implemented method of  claim 1 , wherein the graphical representation of the genomic data is a first graphical representation of genomic data of a first chromosome;
 the method further comprising displaying, by the computing system, a second graphical representation of genomic data of a different, second chromosome, the second graphical representation comprising one or more tracks that are arranged to show one or more features of the genomic data of the second chromosome for at least one organism.   
     
     
         3 . The computer-implemented method of  claim 2 , further comprising determining, by the computing system, syntenic regions of the genomic data of the first chromosome and the genomic data of the second chromosome; and
 Outputting, by the computing system for display on the graphical user interface, graphical elements that connect the first graphical representation and the second graphical representation, and that show corresponding syntenic regions of the genomic data of the first chromosome and the genomic data of the second chromosome.   
     
     
         4 . The computer-implemented method of  claim 1 , further comprising identifying that user input has entered a search query associated with a particular organism; and
 retrieving, by the computing system, a set of search results that are determined to be responsive to the search query, each search result in the set of search results indicating a respective chromosomal sequence location for the particular organism.   
     
     
         5 . The computer-implemented method of  claim 4 , further comprising generating and outputting for display on the graphical user interface, by the computing system, a graphical representation of one or more chromosomes for the particular organism that shows graphical markers at locations of the one or more chromosomes that correspond to the respective chromosomal sequence locations indicated by the set of search results. 
     
     
         6 . The computer-implemented method of  claim 4 , further comprising:
 receiving, by the computing system, an indication that user input selected a first search result from among the set of search results; and   automatically displaying, by the computing system, a graphical representation of the genomic data for the particular organism that shows a zoomed-in region corresponding to the location of the chromosome indicated by the first search result.   
     
     
         7 . The computer-implemented method of  claim 1 , further comprising:
 receiving, by the computing system, an indication that the designation of the reference organism is changed from the first organism to the second organism; and   dynamically modifying, by the computing system, the graphical user interface by:
 re-ordering, by the computing system, the plurality of tracks in the graphical representation of the genomic data so that the second track that shows the first particular feature of the second organism is shown in the reference position of the graphical representation, the first and third tracks are shown in respective positions outside of the reference position, and the first particular features of the first and third tracks are each shown relative to the first particular features of the second track. 
   
     
     
         8 . The computer-implemented method of  claim 7 , wherein re-ordering the plurality of tracks in the graphical representation comprises automatically arranging, by the computing system, the plurality of tracks in descending order of determined genetic similarity between the second organism, due to the second organism being designated as the reference organism, and the corresponding organisms for each of the other tracks in the plurality of tracks, so that tracks corresponding to organisms that are more genetically similar to the second organism are caused to be shown in closer proximity to the second track and tracks corresponding to organisms that are less genetically similar to the second organism are caused to be shown a further distance from the second track. 
     
     
         9 . The computer-implemented method of  claim 7 , further comprising determining, by the computing system, the genetic similarities between the second organism and the corresponding organisms for each of the other tracks in the plurality of tracks based only on data for a portion of the chromosomal sequence of the organisms currently being outputted for display. 
     
     
         10 - 25 . (canceled) 
     
     
         26 . One or more non-transitory computer-readable devices having instructions stored thereon that, when executed by one or more processors, cause performance of operations comprising:
 generating, by a computing system and based at least on genomic data for the plurality of organisms received by the computing system, a graphical user interface having a graphical representation of the genomic data, the graphical representation comprising:
 a plurality of tracks that are arranged to show one or more features of the genomic data for each organism wherein the plurality of tracks includes a first track that shows a first particular feature of a first organism, a second track that shows the first particular feature of a second organism, and a third track that shows the first particular feature of a third organism: 
   identifying, by the computing system, that the first organism is designated as a reference organism;   dynamically modifying, by the computing system, the graphical user interface by ordering the plurality of tracks in the graphical representation of the genomic data so that:
 the first track that shows the first particular feature of the first organism is shown in a reference position of the graphical representation, 
 the second and third tracks are shown in respective positions outside of the reference position, and 
 the first particular features of the second and third tracks are each shown 
 relative to the first particular features of the first track. 
   
     
     
         27 - 36 . (canceled) 
     
     
         37 . The one or more non-transitory computer-readable devices of  claim 26 , wherein:
 the first particular feature comprises single nucleotide polymorphisms (SNPs); and   the operations further comprise generating, by the computing system, the graphical representation of the genomic data so that the second track shows, as a result of the first organism being designated as the reference organism, SNPs in the genomic data of the second organism relative to the genomic data of the first organism shown in the first track.   
     
     
         38 . The one or more non-transitory computer-readable devices of  claim 37 , wherein the second track shows SNPs in the genomic data of the second organism relative to the genomic data of the first organism by showing colored elements along the second track at locations that correspond to locations in a chromosome sequence where SNPs occur that are opposite of SNPs in the genomic data of the first organism. 
     
     
         39 . The one or more non-transitory computer-readable devices of  claim 26 , wherein the operations further comprise obtaining, at the computing system, data that indicates expression levels for corresponding portions of the genomic data for one or more of the plurality of organisms. 
     
     
         40 . The one or more non-transitory computer-readable devices of  claim 39 , wherein:
 the first particular feature comprises the expression levels for the corresponding portions of the genomic data,   the operations further comprise generating, by the computing system, the graphical representation of the genomic data so that the second track shows, as a result of the first organism being designated as the reference organism, expression levels for the corresponding portions of the genomic data of the second organism relative to the expression levels of for the corresponding portions of the genomic data of the first organism.   
     
     
         41 . (canceled) 
     
     
         42 . The one or more non-transitory computer-readable devices of  claim 39 , wherein the operations further comprise:
 dynamically modifying, by the computing system, the graphical user interface by:
 generating, and based at least on the data that indicates the expression levels for the corresponding portions of the genomic data for the one or more of the plurality of organisms, a multidimensional plot showing variability in expression levels among different sets of expression data for particular ones of the plurality of organisms. 
   
     
     
         43 . The one or more non-transitory computer-readable devices of  claim 42 , wherein generating the multidimensional plot comprises automatically limiting the plot to showing only expression levels of sequences corresponding to a portion the genomic data being outputted for display in the graphical representation of the genomic data, to the exclusion of expression levels of sequences outside of the portion of the genomic data being outputted for display in the graphical representation of the genomic data. 
     
     
         44 . The one or more non-transitory computer-readable devices of  claim 26 , wherein the first particular feature comprises at least one of quantitative trait loci (QTLs) and trait linkage scores for particular sequence locations. 
     
     
         45 . The one or more non-transitory computer-readable devices of  claim 26 , wherein:
 the first particular feature comprises CpG islands; and   the operations further comprise generating, by the computing system, the graphical representation of the genomic data so that at least one of the plurality of tracks shows locations of CpG islands within the genomic data for a corresponding organism.   
     
     
         46 . The one or more non-transitory computer-readable devices of  claim 26 , wherein the plurality of tracks includes a fourth track that shows the first particular feature of a fourth organism;
 the method, wherein the operations further comprise:   identifying, by the computing system, that the fourth organism is designated as a second reference organism; and   dynamically modifying, by the computing system, the graphical user interface by:
 ordering, based on the first organism being designated as the reference organism, the plurality of tracks in the graphical representation of the genomic data so that the fourth track is shown in a second reference position of the graphical representation, and the first particular features of the second and third tracks are each shown relative to both the first particular features of the first track and the first particular features of the fourth track. 
   
     
     
         47 - 50 . (canceled) 
     
     
         51 . A computer program product, stored on one or more non-transitory computer-readable devices, for analyzing and representing genome-related biological data, the program product including:
 a genotype tracks module configured to generate and output for display one or more tracks showing features of genomic data for corresponding organisms;   a similarity analyzer configured to determine similarities between corresponding portions of genetic sequences for a reference organism and two or more additional organisms; and   a track arrangement module configured to order the one or more tracks for display based on the determined similarities between the corresponding portions of genetic sequences for the reference organism and the two or more additional organisms.   
     
     
         52 . (canceled)