CN102902817B - Public animal bifidobacterium probiotics codon database management method - Google Patents
Public animal bifidobacterium probiotics codon database management method Download PDFInfo
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- CN102902817B CN102902817B CN201210411125.4A CN201210411125A CN102902817B CN 102902817 B CN102902817 B CN 102902817B CN 201210411125 A CN201210411125 A CN 201210411125A CN 102902817 B CN102902817 B CN 102902817B
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Abstract
The invention discloses a public animal bifidobacterium probiotics codon database management method. The management method comprises the following steps of: receiving an instruction, and calling a public animal bifidobacterium database management system; selecting animal bifidobacterium; selecting a compiling sequence through codon analysis software CodonW and a text editor; and acquiring all codon data of 18035 coding sequences. The defects in the prior art are overcome, and a public animal bifidobacterium probiotics codon database management system is invented. According to the database technology and network, the codon data of different animal bifidobacterium are acquired by means of the codon analysis software CodonW, the codon data of bifidobacterium of seven animals is saved, and the data is conveniently queried by related workers.
Description
Technical field
The invention belongs to database management technology field, particularly relate to a kind of public animal bifidobacteria probio codon database management method.
Background technology
The formation amino acid of protein and the kind of encode codons are various, there is degeneracy in codon, such as leucine is encoded by six kinds of codons, and the amino acid whose codon of encode most is called as synonym, nonrandom during the use of synonym, there is Preference.So far, eucaryote, prokaryotes and even virus all find the Preference of codon, and codon preference Producing reason is considered to mainly comprise two, i.e. mutation pressure and translational selection.Animal bifidobacteria is added in dairy products can contribute to intestinal health, pharmaceutically having extensive use, so far, rare database covers the codon data of detailed Bifidobacterium, at the physiology of Bifidobacterium, in cytology, science of heredity, molecular evolution, molecular biology and even actual production operation, sometimes all need the codon data of inquiring about Bifidobacterium.But, there is no a publicly available complete Bifidobacterium codon database up to now and occur, bring great inconvenience to related work person.
Summary of the invention
This programme, in order to overcome the deficiencies in the prior art, has invented public animal bifidobacteria codon database management system.By database technology and network, obtain the codon data of different animals Bifidobacterium by codon analysis software CodonW, realize filing to the codon data of seven kinds of animal bifidobacterias, person inquires about use to facilitate related work.
The embodiment of the present invention is achieved in that a kind of public animal bifidobacteria probio codon database management method, and it is characterized in that, this management method comprises the following steps:
Double-click and run public animal bifidobacteria data base management system (DBMS);
Select animal bifidobacteria;
Compiling sequence is selected by codon analysis software CodonW and text editor;
Obtain all codon data of 18035 coded sequences; .
Further, public animal bifidobacteria data base management system (DBMS) establishes seven forms, cover the animal bifidobacteria that seven kinds of full-length gene groups are available, all seven forms are through the comprehensive form of the information content of test of many times design, the codon data of coded sequence is all comprised wherein, by integrating, define database, database has based on the visualized operation interface under windows 7 system, user can enter into corresponding interface by selecting different objects, and each object is strictly linked to corresponding list or form.
Further, seven kinds of animals are respectively: Iactis AD011, Iactis BB-12, IactisBLC1, Iactis CNCM 1-2494, Iactis DSM 10140, Iactis V9, Iactis B1-04.
Further, coded sequence must comprise at least 50 codons, there is certain association, be specially: the adenine content (A of codon the 3rd between codon data
3s), the thymine content (T that codon is the 3rd
3s), the guanine content (G of codon the 3rd
3s), the cytosine content (C that codon is the 3rd
3s), codon the 3rd GC content (GC
3s), codon effective quantity (Nc), the correlation coefficient of amino acid length (Laa) and gene coordinate (Axis).
Further, 18035 coded sequences are had.
The invention provides a kind of public animal bifidobacteria codon database management system that can utilize the Internet download, be a kind of efficient, convenient, comprehensively, rationally, the data base management system (DBMS) of friendly interface of showing consideration for.By running the animal bifidobacteria data base management system (DBMS) set up in computer, this database is list interactive interface, user can carry out the corresponding codon data of inquiry by selecting a coded sequence, database comprises the codon data of seven kinds of animal bifidobacterias, is stored in design respectively in the middle of seven forms of test of many times.First the animal bifidobacteria kind of required inquiry is selected, compiling sequence is selected and then by CodonW and text editor, obtain all codon data of 18035 coded sequences, all codon data of each coded sequence must be complete, the thymine content that codon is the 3rd, the cytosine content that codon is the 3rd, the adenine content that codon is the 3rd, the guanine content that codon is the 3rd, codon adaptability index, codon preference index, optimal codon frequency, codon effective quantity, codon the 3rd GC content, synonym frequency, amino acid length, water wettability and the aromaticity information of protein must comprise, required information can be inquired about by operating user above and carry out bookkeeping on computers.
Accompanying drawing explanation
Fig. 1 is the process flow diagram of public animal bifidobacteria codon database management method provided by the invention.
Embodiment
In order to make object of the present invention, technical scheme and advantage clearly understand, below in conjunction with drawings and Examples, the present invention is further elaborated.Should be appreciated that specific embodiment described herein only in order to explain the present invention, be not intended to limit the present invention.
Fig. 1 shows public animal bifidobacteria codon database management system provided by the invention, and this system comprises:
In step S101, receive instruction, call public animal bifidobacteria data base management system (DBMS);
Required hardware is microcomputer; Pentium (R) Dua l-Core CPU, 2.00GB internal memory; Required software is Microsoft windows 7 Ultimate, Microsoft Visual FoxPro 9.0 Chinese edition, Microsoft office 2007.
In step s 102, animal bifidobacteria is selected;
Public animal bifidobacteria data base management system (DBMS) establishes seven forms, cover the animal bifidobacteria that seven kinds of full-length gene groups are available, all seven forms are through the comprehensive form of the information content of test of many times design, the codon data of coded sequence is all comprised wherein, by integrating, define database, database has based on the visualized operation interface under windows 7 system, user can enter into corresponding interface by selecting different objects, and each object is strictly linked to corresponding list or form.Seven kinds of animals are respectively: Iactis AD011, Iactis BB-12, Iactis BLC1, Iactis CNCM 1-2494, and IactisDSM 10140, Iactis V9, Iactis B1-04 are as shown in table 1 below.
In step s 103, compiling sequence is selected by codon analysis software CodonW and text editor; One has 18035 coded sequences.
In step S104, obtain all codon data of 18035 coded sequences;
Coded sequence must comprise at least 50 codons, there is certain association, be specially: the adenine content (A of codon the 3rd between codon data
3s), the thymine content (T that codon is the 3rd
3s), the guanine content (G of codon the 3rd
3s), the cytosine content (C that codon is the 3rd
3s), codon the 3rd GC content (GC
3s), codon effective quantity (Nc), the correlation coefficient of amino acid length (Laa) and gene coordinate (Axis)
Run the animal bifidobacteria data base management system (DBMS) set up in computer, this database is list interactive interface, user can carry out the corresponding codon data of inquiry by selecting a coded sequence, database comprises the codon data of seven kinds of animal bifidobacterias, is stored in design respectively in the middle of seven forms of test of many times.First the animal bifidobacteria kind of required inquiry is selected, compiling sequence is selected and then by CodonW and text editor, obtain all codon data of 18035 coded sequences, all codon data of each coded sequence must be complete, the thymine content that codon is the 3rd, the cytosine content that codon is the 3rd, the adenine content that codon is the 3rd, the guanine content that codon is the 3rd, codon adaptability index, codon preference index, optimal codon frequency, codon effective quantity, codon the 3rd GC content, synonym frequency, amino acid length, water wettability and the aromaticity information of protein must comprise, required information can be inquired about by operating user above and carry out bookkeeping on computers.
The invention provides a kind of public animal bifidobacteria codon database management system that can utilize the Internet download, be a kind of efficient, convenient, comprehensively, rationally, the data base management system (DBMS) of friendly interface of showing consideration for.By running the animal bifidobacteria data base management system (DBMS) set up in computer, this database is list interactive interface, user can carry out the corresponding codon data of inquiry by selecting a coded sequence, database comprises the codon data of seven kinds of animal bifidobacterias, is stored in design respectively in the middle of seven forms of test of many times.First the animal bifidobacteria kind of required inquiry is selected, compiling sequence is selected and then by CodonW and text editor, obtain all codon data of 18035 coded sequences, all codon data of each coded sequence must be complete, the thymine content that codon is the 3rd, the cytosine content that codon is the 3rd, the adenine content that codon is the 3rd, the guanine content that codon is the 3rd, codon adaptability index, codon preference index, optimal codon frequency, codon effective quantity, codon the 3rd GC content, synonym frequency, amino acid length, water wettability and the aromaticity information of protein must comprise, required information can be inquired about by operating user above and carry out bookkeeping on computers.
The raising that this system is predictive genes level and the enhancement of target gene expression provide a solid foundation, and provide the codon data of probio animal bifidobacteria, can provide reference for the mechanism exploring probio; The related work persons such as molecular biologist, geneticist, molecular evolution scholar, food and nutritionist can be allowed can to inquire about the animal bifidobacteria codon data needed for oneself whenever and wherever possible by the instrument such as notebook computer, mobile phone; This scheme can be widely used in the field such as biomedicine and food nutrition.
The foregoing is only preferred embodiment of the present invention, not in order to limit the present invention, all any amendments done within the spirit and principles in the present invention, equivalent replacement and improvement etc., all should be included within protection scope of the present invention.
Claims (1)
1. a public animal bifidobacteria probio codon database management method, it is characterized in that, this management method comprises the following steps:
Receive instruction, call public animal bifidobacteria data base management system (DBMS);
Select animal bifidobacteria;
Compiling sequence is selected by codon analysis software CodonW and text editor;
Obtain all codon data of 18035 coded sequences;
Public animal bifidobacteria data base management system (DBMS) establishes seven forms, cover the animal bifidobacteria that seven kinds of full-length gene groups are available, all seven forms are through the comprehensive form of the information content of test of many times design, the codon data of coded sequence is all comprised wherein, by integrating, define database, database has based on the visualized operation interface under windows 7 system, user can enter into corresponding interface by selecting different objects, and each object is strictly linked to corresponding list or form;
Seven kinds of animals are respectively: Iactis AD011, Iactis BB-12, Iactis BLC1, Iactis CNCM 1-2494, Iactis DSM10140, Iactis V9, IactisB1-04;
Coded sequence must comprise at least 50 codons, certain association is there is between codon data, be specially: the adenine content (A3s) of codon the 3rd, the thymine content (T3s) of codon the 3rd, the guanine content (G3s) of codon the 3rd, the cytosine content (C3s) of codon the 3rd, codon the 3rd GC content (GC3s), codon effective quantity (Nc), the correlation coefficient of amino acid length (Laa) and gene coordinate (Axis);
Have 18035 coded sequences.
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| Application Number | Priority Date | Filing Date | Title |
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| CN201210411125.4A CN102902817B (en) | 2012-10-14 | 2012-10-14 | Public animal bifidobacterium probiotics codon database management method |
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| CN201210411125.4A CN102902817B (en) | 2012-10-14 | 2012-10-14 | Public animal bifidobacterium probiotics codon database management method |
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| CN102902817A CN102902817A (en) | 2013-01-30 |
| CN102902817B true CN102902817B (en) | 2015-05-06 |
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Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1598821A (en) * | 2004-09-07 | 2005-03-23 | 东南大学 | Seaching method of genome sequence data based on characteristic |
| US7702464B1 (en) * | 2001-08-21 | 2010-04-20 | Maxygen, Inc. | Method and apparatus for codon determining |
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2012
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Patent Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US7702464B1 (en) * | 2001-08-21 | 2010-04-20 | Maxygen, Inc. | Method and apparatus for codon determining |
| CN1598821A (en) * | 2004-09-07 | 2005-03-23 | 东南大学 | Seaching method of genome sequence data based on characteristic |
Non-Patent Citations (1)
| Title |
|---|
| "长双歧杆菌NCC2705 葡萄糖与乳糖代谢的比较蛋白质组学";何湘等;《微生物学报》;20081104;第1451-1458页 * |
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