Functional sequence selection method and functional sequence selection system

Patent metadata

Field	Value
Publication number	US-2020327958-A1
Application number	US-202016824365-A
Country	US
Kind code	A1
Filing date	Mar 19, 2020
Priority date	Mar 22, 2019
Publication date	Oct 15, 2020
Grant date	—

Abstract

A method for making a recombinant gene includes searching a database using a nucleotide sequence of a coding region, a nucleotide sequence that encodes an amino acid sequence, or an amino acid sequence, of a gene, for one or more nucleotide sequences having homology; selecting one or more nucleotide sequences other than nucleotide sequences only derived from a genome from the selected nucleotide sequences; for ones of the selected one or more nucleotide sequences comprising an upstream or downstream nucleotide sequence, analyzing whether the upstream or downstream nucleotide sequence is a functional sequence to select one or more first functional sequences; for ones of the selected one or more nucleotide sequences comprising no upstream or downstream nucleotide sequence, analyzing whether a gene information has any description indicating a functional sequence to select one or more second functional sequences; scoring the selected functional sequences; and selecting one or more functional sequences.

First claim

1 . A functional sequence selection method for making a recombinant gene for expressing a gene of interest in a cell using a database comprising one or more data elements comprising a sequence of a gene or a part of the gene, an amino acid sequence encoded by a gene or a part of the amino acid sequence and/or a gene information of the gene, the method comprising the steps of, in a functional sequence selection system comprising
an input device for inputting, as a query, a nucleotide sequence of a coding region of the gene of interest, an amino acid sequence of the gene of interest, or a part thereof; a selection device for selecting a functional sequence; and an output device for outputting the selected functional sequence; inputting a query with the input device; in the selection device, searching the database, with homologous sequence search means, using a nucleotide sequence of a coding region, a nucleotide sequence that encodes an amino acid sequence, or an amino acid sequence, of a gene of interest, for one or more nucleotide sequences having homology to the nucleotide sequence of the coding region of the gene of interest or the nucleotide sequence that encodes the amino acid sequence of the gene of interest; memorizing, with first sequence list memorizing means, the one or more nucleotide sequences obtained by the search as a first sequence list; removing, with functional sequence selecting means, nucleotide sequences only derived from a genome to select one or more nucleotide sequences other than the nucleotide sequences only derived from a genome;
(1) for ones of the selected one or more nucleotide sequences comprising a nucleotide sequence upstream or downstream of a region homologous to the nucleotide sequence or the nucleotide sequence that encodes an amino acid used for the search, analyzing whether the upstream or downstream nucleotide sequence is a functional sequence to select one or more first functional sequences, and
(2) for ones of the selected one or more nucleotide sequences comprising no nucleotide sequence upstream and downstream of a region homologous to the nucleotide sequence or the nucleotide sequence that encodes an amino acid used for the search, analyzing by search whether the gene information in the data element comprises any description indicating a functional sequence to select one or more second functional sequences;
memorizing, with second sequence list memorizing means, a second sequence list comprising the one or more first functional sequences and the one or more second functional sequences; scoring, with scoring means, the first and second functional sequences in the second sequence list; selecting, with functional sequence selection means, one or more functional sequences at high ranks in the scoring result; memorizing, with functional sequence memorizing means, the selected one or more functional sequences at high ranks; and outputting, with the output device, the selected one or more functional sequences at higher ranks.

2 . The functional sequence selection method according to claim 1 , wherein the one or more nucleotide sequences other than the nucleotide sequences only derived from a genome are selected by analyzing whether the gene information comprises any keyword representing a nucleotide sequence derived from a genome.

3 . The functional sequence selection method according to claim 1 , wherein the functional sequence comprises a promoter sequence, a terminator sequence, and a stop codon.

4 . The functional sequence selection method according to claim 1 , wherein in the case of (1), whether the upstream or downstream nucleotide sequence is a functional sequence is analyzed using a functional sequence library or the gene information.

5 . The functional sequence selection method according to claim 1 , wherein the first and second functional sequences are scored according to frequencies of occurrence or according to frequency of a given keyword in the gene information in the data element to which each functional sequence is relevant.

6 . The functional sequence selection method according to claim 1 , further comprising the step of removing one or more functional sequences that are naturally occurring in the gene of interest from the first and second functional sequences before scoring the first and second functional sequences.

7 . A functional sequence selection system for making a recombinant gene for expressing a gene of interest in a cell using a database comprising one or more data elements comprising a sequence of a gene or a part of the gene, an amino acid sequence encoded by a gene or a part of the amino acid sequence and/or a gene information of the gene, the system comprising:
an input device for inputting, as a query, a nucleotide sequence of a coding region of the gene of interest, an amino acid sequence of the gene of interest, or a part thereof; a selection device for selecting a functional sequence, the selection device comprising:
homologous sequence search means for searching the database, using a nucleotide sequence of a coding region, a nucleotide sequence that encodes an amino acid sequence, or an amino acid sequence, of a gene of interest, for one or more nucleotide sequences having homology to the nucleotide sequence of the coding region of the gene of interest or the nucleotide sequence that encodes the amino acid sequence of the gene of interest;
first sequence list memorizing means for storing the one or more nucleotide sequences obtained by the search as a first sequence list;
functional sequence selecting means for removing nucleotide sequences only derived from a genome to select one or more nucleotide sequences other than the nucleotide sequences only derived from a genome,
(1) for ones of the selected one or more nucleotide sequences comprising a nucleotide sequence upstream or downstream of a region homologous to the nucleotide sequence or the nucleotide sequence that encodes an amino acid used for the search, analyzing whether the upstream or downstream nucleotide sequence is a functional sequence to select one or more first functional sequences, and
(2) for ones of the selected one or more nucleotide sequences comprising no nucleotide sequence upstream and downstream of a region homologous to the nucleotide sequence or the nucleotide sequence that encodes an amino acid used for the search, analyzing by search whether the gene information in the data element comprises any description indicating a functional sequence to select one or more second functional sequences;

second sequence list memorizing means for memorizing a second sequence list comprising the one or more first functional sequences and the one or more second functional sequences;
scoring means for scoring the first and second functional sequences in the second sequence list;
functional sequence selection means for selecting one or more functional sequences at higher ranks in the scoring result; and
functional sequence memorizing means for storing the selected one or more functional sequences at higher ranks; and
an output device for outputting the selected functional sequence.

8 . The functional sequence selection system according to claim 7 , wherein the one or more nucleotide sequences other than the nucleotide sequences only derived from a genome are selected by analyzing whether the gene information comprises any keyword representing a nucleotide sequence derived from a genome.

9 . The functional sequence selection system according to claim 7 , wherein the functional sequence comprises a promoter sequence, a terminator sequence, and a stop codon.

10 . The functional sequence selection system according to claim 7 , wherein
in the case of (1), wheth

Assignees

• Hitachi Ltd
• Univ Kobe Nat Univ Corp
• Univ Kyoto

Inventors

• Tanabe Maiko
• Takeda Shizu
• Ito Kiyoto
• Imaichi Osamu
• Tsuge Kenji
• Araki Michihiro

Classifications

• G16B20/00

  ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations · CPC title

• G16B30/00 Primary

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• G16B35/20

  Screening of libraries · CPC title

• G16B25/10 Primary

  Gene or protein expression profiling; Expression-ratio estimation or normalisation · CPC title