Systems and methods for automated annotation and screening of biological sequences

A biological sequence, automatic generation technology, applied in general control system, sequence analysis, bioinformatics, etc., can solve problems such as lack of

Pending Publication Date: 2019-04-02
TWIST BIOSCI
View PDF6 Cites 0 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

For a given protein, there is a lack of centralized information sources that focus on the possibility of causing harm to it and the scenarios under which such harm may occur

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Systems and methods for automated annotation and screening of biological sequences
  • Systems and methods for automated annotation and screening of biological sequences
  • Systems and methods for automated annotation and screening of biological sequences

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0108] Example 1: Sequence Annotation

[0109] A biological sequence is received by a processor unit. In this embodiment, the biological sequence is a protein sequence. The processor unit accesses the protein database and identifies protein sequences that match the received protein sequences. The processor unit receives information related to various features of the protein sequence. Features include: nucleic acid sequence related to protein sequence, protein sequence, protein name, strain source information, link to sequence database (e.g., NCBI), sequence database accession number, identical sequence (protein or nucleic acid), similar sequence (protein or nucleic acid), source of disease (e.g., virus, bacteria), taxonomic description of the organism (e.g., kingdom, phylum, class, order, family, genus, species), host information (e.g., human, mammal, bird , insects), scenario or route of harmful interaction (eg, ingestion, inhalation), symptoms and degree of concern. In t...

Embodiment 2

[0112] Example 2: Sequence Screening

[0113] refer to Figure 3A , the processor receives machine instructions in the form of a query file containing biological sequence information, in this case nucleic acid information. The processor also communicates with nucleic acid and protein databases. The processor accesses nucleic acid and protein databases. A BLAST-processed report is generated listing identical and similar sequences identified as being related to some or all of the queried biological sequence. Sequences from the BLAST-processed reports are then queried against databases containing sequence annotations that identify sequences related to pest sequences (proteins or nucleic acids), also referred to as the "restricted" list. A screening report is generated in the form of a user interface summarizing the results of these processes. Screening reports are transmitted in the form of machine instructions for the user interface. The processor receives specific instruct...

Embodiment 3

[0114] Example 3: Prescreening for Specific Genomes

[0115] Access to more than 500 nucleotides in the genome of Variola major or Variola minor is restricted by World Health Organization (WHO) policy. Those who need longer sequences must apply for and obtain permission from the WHO before they can be synthesized. Due to the unique nature of smallpox, only the genomes of variola major and variola minor, as well as vaccinia and other closely related orthopoxviruses, were prescreened. Nucleic acid sequences were evaluated using the general biosafety screening procedure of Example 2 and the genome of orthopoxviruses. This screening occurs in less than 1 second (by blastx on commodity hardware). Vaccinia and other orthopox reference sequences were included to ensure that the requested sequence had maximum homology to smallpox before an alert was issued (similar to the 2010 HHS guidelines 'best match' criteria). This can optionally be done during the order quote generation proce...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

PUM

No PUM Login to view more

Abstract

The present disclosure describes software tools for effective biosecurity based on community knowledge and participation. Annotation tools described herein provide assistance to the synthetic biologycommunity to track emerging science on the link between individual proteins and negative outcomes. Screening tools described herein enables the community to broaden both interest and effective practice of biosecurity so that practitioners and biological sequence or construct providers are empowered to evaluate the safety of order requests rather than waiting until synthesis or even expression. Inaddition, screening tools described herein provide for screening of polynucleotides across the same or multiple orders for sequences associated with harmful biological sequences from a reference database.

Description

[0001] cross reference [0002] This application claims the benefit of U.S. Provisional Patent Application No. 62 / 348,786, filed June 10, 2016, and U.S. Provisional Patent Application No. 62 / 375,858, filed August 16, 2016, each of which is incorporated by reference Incorporated in its entirety. Background technique [0003] Our overall knowledge about individual proteins and biological systems that can pose potential threats to public safety and / or the environment is growing very rapidly. However, this knowledge is widely distributed across different research groups, institutions, and even journals. For a given protein, there is a lack of centralized information sources that focus on the likelihood of causing harm and the scenarios under which such harm may occur. Therefore, new systems and methods are needed to address this challenge. Contents of the invention [0004] Provided herein is a computerized system for providing enhanced polynucleotide synthesis comprising a ...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

Application Information

Patent Timeline
no application Login to view more
Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/00G16B50/00C12N15/10G16B30/10G16B50/30
CPCC12N15/1089G16B99/00G16B30/20G16B30/10G16B50/30G16B35/00G16B50/00C12N15/1068G16B30/00G05B15/00C12N15/10
Inventor 詹姆斯·迪甘斯
Owner TWIST BIOSCI
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap