Precision medicine portal for human diseases

A computer-implemented method comprising:

• receiving a nucleotide string comprising a plurality of nucleotides from at least a portion of one or more individual patients genome, wherein the portion of the genome includes at least one of:
• a 5′-UTR, a promoter, an enhancer, a silencer, an exon, an intron, a coding sequence, a splice acceptor, a splice donor, a branch point site, a 3′-UTR, a Kozak sequence, a poly-A addition site or signal, or a cryptic version thereof, from a known protein coding gene or a non-protein coding RNA gene, and within genes not yet identified in a Dark Matter genome;
• determining a representation of genetic features or elements of the known protein coding gene or the non-protein coding RNA gene on a gene structure in separate modules or tabs of a user interface, by one or more processors executing instructions from at least one of Shapiro-Senapathy, MaxEntScan, and NNSplice algorithms to compute scores for real and cryptic splice acceptor and donor sites, branch point sites, promoters, 5′ and 3′ UTRs, and poly-A sites or signals using PWMs;
• overlaying, on the user interface, variants from the one or more individuals on each of the genetic elements depicted on the gene structure or in a sequence view, and rendering, on user interaction, aligned sequence read evidence with read counts and allele-frequency values from SAM/BAM and VCF files, and automatically updating overlays and evidence in real time responsive to user interactions and availability of updated analysis outputs;
• and,
• providing, on the user interface, a graphic depiction of a mutational impact comprising a defect in the genetic elements, domain, biochemical function, or protein structure, or a transcriptional, translational or splicing aberration in the gene structure or sequence, or a protein structure or sequence.

A computer-implemented method comprising:

• receiving a nucleotide string comprising a plurality of nucleotides from at least a portion of one or more individual patients genome, wherein the portion of the genome includes at least one of:
• a 5′-UTR, a promoter, an enhancer, a silencer, an exon, an intron, a coding sequence, a splice acceptor, a splice donor, a branch point site, a 3′-UTR, a Kozak sequence, a poly-A addition site or signal, or a cryptic version thereof, from a known protein coding gene or a regulatory, splicing, or functional element of a non-protein coding RNA gene, and within the genes not yet identified in a Dark Matter genome;
• providing, via a display, a first graphical representation of a chromosome or a genome on a single line drawn to scale within a view of a computer or expanded view;
• providing, via the display, a second graphical representation of protein coding genes or non-protein coding RNA genes contained in a chromosome or a genome on the single line;
• and
• depicting, via the display, separate features comprising variations, mutations, consequences, genes, genetic elements, diseases, domains, biochemical functions, zygosity, or other genetically or clinically relevant features, details, or their frequencies, from the one or more individual patients in separate graphical notations, and overlaying, on multi-track genome-scale single lines, variants and rendering, in interactive popovers and mouseovers, aligned sequence read evidence with read counts and allele-frequency values from SAM/BAM and VCF files, and automatically updating overlays and evidence in real time responsive to user interactions and availability of updated analysis outputs.