CN102902817A - Public animal bifidobacterium probiotics codon database management method - Google Patents
Public animal bifidobacterium probiotics codon database management method Download PDFInfo
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- CN102902817A CN102902817A CN2012104111254A CN201210411125A CN102902817A CN 102902817 A CN102902817 A CN 102902817A CN 2012104111254 A CN2012104111254 A CN 2012104111254A CN 201210411125 A CN201210411125 A CN 201210411125A CN 102902817 A CN102902817 A CN 102902817A
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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 the database management technology field, relate in particular to a kind of public animal bifidobacteria probio codon data base management method.
Background technology
It is various consisting of the amino acid of protein and the kind of coding password, there is degeneracy in codon, and for example leucine is encoded by six kinds of codons, and the amino acid whose codon of the same race of encoding is called as synonym, nonrandom during the use of synonym, there is Preference.So far, eucaryote, prokaryotes and even virus are all found the Preference of codon, and the reason that codon preference produces is considered to mainly comprise two, i.e. mutation pressure and translation selected.Animal bifidobacteria is added in the dairy products can help intestinal health, pharmaceutically having extensive use, so far, rare database has been contained the codon data of detailed Bifidobacterium, at the physiology of Bifidobacterium, sometimes all need to inquire about the codon data of Bifidobacterium in cytology, science of heredity, molecular evolution, molecular biology and even the actual production operation.Yet, there is no up to now a publicly available complete Bifidobacterium codon database and occur, brought great inconvenience for the related work person.
Summary of the invention
This programme has been invented public animal bifidobacteria codon data base management system (DBMS) in order to overcome the deficiencies in the prior art.By database technology and network, obtain the codon data of different animals Bifidobacterium by codon analysis software CodonW, realize the codon data of seven kinds of animal bifidobacterias is filed, the person inquires about use to make things convenient for the related work.
The embodiment of the invention is achieved in that a kind of public animal bifidobacteria probio codon data base management method, it is characterized in that, this management method may further comprise the steps:
Double-click the public animal bifidobacteria data base management system (DBMS) of operation;
Select animal bifidobacteria;
Select the compiling sequence 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) has been set up seven forms, seven kinds of animal bifidobacterias that the full-length gene group is available have been contained, all seven forms are the comprehensive forms of the information content through the test of many times design, the codon data of coded sequence is all comprised wherein, by integrating, formed database, database has based on the visualized operation interface under windows 7 systems, the user can enter into corresponding interface by selecting different objects, and each object strictly is linked to corresponding list or form.
Further, seven kinds of animals are respectively: Iactis AD011, Iactis BB-12, Iactis BLC1, Iactis CNCM 1-2494, Iactis DSM 10140, Iactis V9, Iactis B1-04.
Further, coded sequence must comprise at least 50 codons, has certain association between the codon data, is specially: the tertiary adenine content of codon (A
3s), the tertiary thymine content of codon (T
3s), the tertiary guanine content of codon (G
3s), the tertiary cytimidine content of codon (C
3s), the 3rd GC content (GC of codon
3s), the effective quantity of codon (Nc), the correlation coefficient of amino acid length (Laa) and gene coordinate (Axis).
Further, have 18035 coded sequences.
The invention provides a kind of public animal bifidobacteria codon data base management system (DBMS) that can utilize the Internet download, be a kind of efficient, convenient, comprehensively, rationally, the data base management system (DBMS) of the friendly interface shown consideration for.By the animal bifidobacteria data base management system (DBMS) of setting up in the operation computer, this database is the list interactive interface, the user can be by selecting a corresponding codon data of coded sequence inquiry, database comprises the codon data of seven kinds of animal bifidobacterias, is stored in respectively design through in the middle of seven forms of test of many times.At first select the animal bifidobacteria kind of required inquiry, select the compiling sequence by CodonW and text editor and then, obtain all codon data of 18035 coded sequences, all codon data of each coded sequence must be complete, the tertiary thymine content of codon, the tertiary cytimidine content of codon, the tertiary adenine content of codon, the tertiary guanine content of codon, codon adaptability index, the codon preference index, the optimal codon frequency, the effective quantity of codon, the 3rd GC content of codon, the synonym frequency, amino acid length, the water wettability of protein and aromaticity information must comprise; Can inquire about required information and manage on computers operation by above operation user.
Description of drawings
Fig. 1 is the process flow diagram of public animal bifidobacteria codon data base management method provided by the invention.
Embodiment
In order to make purpose of the present invention, technical scheme and advantage clearer, 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, is not intended to limit the present invention.
Fig. 1 has demonstrated public animal bifidobacteria codon data base management system (DBMS) 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 Ultimates, Microsoft Visual FoxPro 9.0 Chinese editions, Microsoft office 2007.
In step S102, select animal bifidobacteria;
Public animal bifidobacteria data base management system (DBMS) has been set up seven forms, seven kinds of animal bifidobacterias that the full-length gene group is available have been contained, all seven forms are the comprehensive forms of the information content through the test of many times design, the codon data of coded sequence is all comprised wherein, by integrating, formed database, database has based on the visualized operation interface under windows 7 systems, the user can enter into corresponding interface by selecting different objects, and each object strictly is linked to corresponding list or form.Seven kinds of animals are respectively: Iactis AD011, and Iactis BB-12, Iactis BLC1, Iactis CNCM 1-2494, Iactis DSM 10140, Iactis V9, Iactis B1-04, as shown in table 1 below.
In step S103, select the compiling sequence 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, has certain association between the codon data, is specially: the tertiary adenine content of codon (A
3s), the tertiary thymine content of codon (T
3s), the tertiary guanine content of codon (G
3s), the tertiary cytimidine content of codon (C
3s), the 3rd GC content (GC of codon
3s), the effective quantity of codon (Nc), the correlation coefficient of amino acid length (Laa) and gene coordinate (Axis)
The animal bifidobacteria data base management system (DBMS) of setting up in the operation computer, this database is the list interactive interface, the user can be by selecting a corresponding codon data of coded sequence inquiry, database comprises the codon data of seven kinds of animal bifidobacterias, is stored in respectively design through in the middle of seven forms of test of many times.At first select the animal bifidobacteria kind of required inquiry, select the compiling sequence by CodonW and text editor and then, obtain all codon data of 18035 coded sequences, all codon data of each coded sequence must be complete, the tertiary thymine content of codon, the tertiary cytimidine content of codon, the tertiary adenine content of codon, the tertiary guanine content of codon, codon adaptability index, the codon preference index, the optimal codon frequency, the effective quantity of codon, the 3rd GC content of codon, the synonym frequency, amino acid length, the water wettability of protein and aromaticity information must comprise; Can inquire about required information and manage on computers operation by above operation user.
The invention provides a kind of public animal bifidobacteria codon data base management system (DBMS) that can utilize the Internet download, be a kind of efficient, convenient, comprehensively, rationally, the data base management system (DBMS) of the friendly interface shown consideration for.By the animal bifidobacteria data base management system (DBMS) of setting up in the operation computer, this database is the list interactive interface, the user can be by selecting a corresponding codon data of coded sequence inquiry, database comprises the codon data of seven kinds of animal bifidobacterias, is stored in respectively design through in the middle of seven forms of test of many times.At first select the animal bifidobacteria kind of required inquiry, select the compiling sequence by CodonW and text editor and then, obtain all codon data of 18035 coded sequences, all codon data of each coded sequence must be complete, the tertiary thymine content of codon, the tertiary cytimidine content of codon, the tertiary adenine content of codon, the tertiary guanine content of codon, codon adaptability index, the codon preference index, the optimal codon frequency, the effective quantity of codon, the 3rd GC content of codon, the synonym frequency, amino acid length, the water wettability of protein and aromaticity information must comprise; Can inquire about required information and manage on computers operation by above operation user.
This system provides a solid foundation for the raising of predictive genes level and the enhancement of target gene expression, and the codon data of probio animal bifidobacteria is provided, and can provide reference for the mechanism of exploring probio; Can allow the related work persons such as molecular biologist, geneticist, molecular evolution scholar, food and nutritionist can inquire about own required animal bifidobacteria codon data whenever and wherever possible by instruments such as notebook computer, mobile phones; This scheme can be widely used in the fields such as biomedicine and food nutrition.
The above only is preferred embodiment of the present invention, not in order to limiting the present invention, all any modifications of doing within the spirit and principles in the present invention, is equal to and replaces and improvement etc., all should be included within protection scope of the present invention.
Claims (5)
1. a public animal bifidobacteria probio codon data base management method is characterized in that, this management method may further comprise the steps:
Receive instruction, call public animal bifidobacteria data base management system (DBMS);
Select animal bifidobacteria;
Select the compiling sequence by codon analysis software CodonW and text editor;
Obtain all codon data of 18035 coded sequences.
2. management method as claimed in claim 1, it is characterized in that, public animal bifidobacteria data base management system (DBMS) has been set up seven forms, seven kinds of animal bifidobacterias that the full-length gene group is available have been contained, all seven forms are the comprehensive forms of the information content through the test of many times design, the codon data of coded sequence is all comprised wherein, by integrating, formed database, database has based on the visualized operation interface under wi ndows 7 systems, the user can enter into corresponding interface by selecting different objects, and each object strictly is linked to corresponding list or form.
3. management method as claimed in claim 2 is characterized in that, seven kinds of animals are respectively: Iactis AD011, Iactis BB-12, Iactis BLC1, Iactis CNCM 1-2494, Iactis DSM10140, Iactis V9, Iactis B1-04.
4. management method as claimed in claim 1 is characterized in that, coded sequence must comprise at least 50 codons, has certain association between the codon data, is specially: the tertiary adenine content of codon (A
3s), the tertiary thymine content of codon (T
3s), the tertiary guanine content of codon (G
3s), the tertiary cytimidine content of codon (C
3s), the 3rd GC content (GC of codon
3s), the effective quantity of codon (Nc), the correlation coefficient of amino acid length (Laa) and gene coordinate (Axis).
5. management method as claimed in claim 1 is characterized in that, has 18035 coded sequences.
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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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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 |
|---|
| 何湘等: ""长双歧杆菌NCC2705 葡萄糖与乳糖代谢的比较蛋白质组学"", 《微生物学报》 * |
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