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.