Identifying genome features in health and disease

A method for identifying a gene in a raw DNA sequence, the method comprising,

• receiving a nucleotide sequence from a reference genome, the reference genome comprising at least one genetic element, wherein the at least one genetic element is selected from a list comprising:
• a 5′-UTR, a promoter, an enhancer, a silencer, an exon, an intron, a coding sequence, a non-protein coding RNA, 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;
• identifying a first exon from the nucleotide sequence, wherein the first exon begins with an initiator codon, wherein the first exon ends with a first donor sequence, and the first exon is bounded by an open reading frame (ORF);
• identifying one or more middle exons from the nucleotide sequence, wherein the middle exon starts with a first acceptor sequence and ends with a second donor sequence, and the middle exon is bounded by the open reading frame (ORF);
• identifying a last exon from the nucleotide sequence, wherein the last exon starts with an acceptor sequence and ends with a stop codon, and the last exon is bounded by the open reading frame (ORF);
• and,
• annotating the splicing and regulatory elements within the gene based on similarity scores or position weight matrix scores.

A computer implemented method, comprising,

• receiving a nucleotide string comprising at least one genetic element, the at least one genetic element selected from one of:
• a 5′-UTR, a promoter, an enhancer, a silencer, an exon, an intron, a coding sequence, a non-protein coding RNA, 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 from a reference genome;
• generating one or more modified nucleotide strings, wherein each base on the one or more modified nucleotide strings is replaced compared to the nucleotide string, wherein replacing each base comprises converting each base to a non-identical nucleotide;
• for the at least one genetic element, calculating the similarity score of the element for every one of the one or more modified nucleotide strings;
• determining overall deleteriousness by comparing the similarity scores for the at least one genetic element for every one of the one or more modified nucleotide strings and for the nucleotide string;
• assigning a molecular effect, the molecular effect selected from one or more of:
• abolition, reduction or enhancement of transcription or translation, exon skipping, intron retention, cryptic exon creation or partial exon deletion due to the deleterious mutation;
• and
• storing the information of the molecular effect for every one or more modified nucleotide strings in a memory.