Unified portal for regulatory and splicing elements for genome analysis

Abstract

A method, including identifying, in a nucleotide string, at least two exons, at least one acceptor, at least one donor, and at least one intron between the at least two exons, is provided. The method includes identifying, in the nucleotide string, a cryptic splice site comprising a sequence of nucleotides based on a similarity score with at least one of the acceptor or the donor, and graphically marking, in a display for a user, the nucleotide string at a location indicative of an exon, an intron, a true splice site, and optionally a cryptic splice site when the similarity score is higher than a pre-selected threshold. A system and a non-transitory, computer-readable medium including instructions to cause the system to perform the method are also provided.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application is a continuation of International Application No. PCT / US2021 / 047025, filed Aug. 20, 2021, entitled “A UNIFIED PORTAL FOR REGULATORY AND SPLICING ELEMENTS FOR GENOME ANALYSIS”, which claims priority under Article 8 of the PCT to U.S. Provisional Application No. 63 / 166,803, entitled “A UNIFIED PORTAL FOR REGULATORY AND SPLICING ELEMENTS FOR GENOME ANALYSIS,” to Sudar Senapathy, filed on Mar. 26, 2021, and to U.S. Provisional Application No. 63 / 166,829, entitled “A PRECISION MEDICINE PORTAL FOR HUMAN DISEASES,” to Periannan Senapathy, filed on Mar. 26, 2021, the contents of both applications incorporated herein by reference in their entirety, for all purposes.[0002]This application is related to International Application No. PCT / US2021 / 047027 filed Aug. 20, 2021, which claims the benefit of U.S. Provisional Patent Application No. 63 / 166,803, filed Mar. 26, 2021, and U.S. Provisional Patent Application No. 63 / 166,829, filed ...

AI Technical Summary

Benefits of technology

The invention includes a computer-implemented method for identifying and marking nucleotide sequences in a genomic data string. The method can identify exons, acceptors, donors, and introns in a nucleotide string, as well as a cryptic splice site or promoter site based on a similarity score with other nucleotides or amino acids. The method can also identify variable nucleotides or allowable nucleotides for a given position in the nucleotide string. This invention can improve the accuracy and efficiency of genomic data analysis and interpretation.

Problems solved by technology

However, little is known as to other portions of the genome that may not encode proteins, but may be linked to disease and other phenotypic traits yet to be discovered.

However, there is a lack of a systematic approach to search, classify, identify, and illustrate coding and non-coding portions of the genome and associated mutations.

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