MySQL common commands

  1. 使用root创建新用户
    insert into
    mysql.user(host, user, password, select_priv, insert_priv, update_priv)
    VALUES (‘localhost’, ‘wangyu’, PASSWORD(‘xxxxxx’), ‘Y’, ‘Y’, ‘Y’);
  2. 更新表记录,以及使更新生效
    UPDATE table SET columnA = ‘Fred’ WHERE columnB = ‘Wilson’
    flush privileges;
  3. 数据库层面
    1. 查看已有数据库
    show databases;
    2. 授权某个用户操作某个数据库
    GRANT privileges ON databasename.tablename TO ‘username’@’host’
    3. 导入数据库
    source filename.sql
    4.查看指定数据库所占空间大小 (Mb)
    SELECT (sum(DATA_LENGTH)+sum(INDEX_LENGTH))/1024/1024 FROM  information_schema.TABLES where TABLE_SCHEMA=’servicer’;
    5. 查看所有表
    show tables;
  4. 表层面
    1. 打印表的内容
    select * from table
    2. 修改表内容
    UPDATE 表名称 SET 列名称 = 新值 WHERE 列名称 = 某值
    3. 打印指定模式的表内容
    select field from table where field like “pattern”;
    %: 通配符,0-N个字符;
    _: 通配符,1个字符;

Arabidopsis thaliana

Arabidopsis thaliana is a small flowering plant of mustard family, brassicaceae (Cruciferae). It is distributed throughout the world and was first reported in the sixteenth century by Johannes Thal. It has been used for over fifty years to study plant mutations and for classical genetic analysis. It is now being used as a model organism to study different aspects of plant biology.
A. thaliana is a diploid plant with 2n = 10 chromosomes. It became the first plant genome to be fully sequenced based on the fact that it has a (1) small genome of ~120 Mb with a simple structure having few repeated sequences (2) short generation time of six weeks from seed germination to seed set, and (3) produces large number of seeds. The sequencing was done by an international collaboration collectively termed the Arabidopsis Genome Initiative (AGI). Though of no economic importance, it is an invaluable resource to agriculturally important crops, particularly to members of the same family, which includes canola, an important source of vegetable oil. EST/mRNA alignments to the Genome are available for ftp download. They are in the Splign format.

Selective Sweep

Sweeps can be categorized in three main categories.

  1. The “classic selective sweep” or “hard selective sweep” is expected to occur when beneficial mutations are rare, but once a beneficial mutation has occurred it increases in frequency rapidly, thereby drastically reducing genetic variation in the population.
  2. A so-called “soft sweep from standing genetic variation” occurs when a previously neutral mutation that was present in a population becomes beneficial because of an environmental change. Such a mutation may be present on several genomic backgrounds so that when it rapidly increases in frequency, it doesn’t erase all genetic variation in the population.
  3. Finally, a “multiple origin soft sweep” occurs when mutations are common (for example in a large population) so that the same or similar beneficial mutations occurs on different genomic backgrounds such that no single genomic background can hitchhike to high frequency.

Genetic terminology

  1. genetic hitchhiking: 遗传搭车
  2. singleton: SNP’s shared by more than one individual indicate levels of relatedness, while SNP’s found only within one individual, referred to as “singletons”, indicate uniqueness.