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利用MISA鉴定简单重复序列(SSR)

楼主收藏举报帖子创建时间: 2018-10-04 00:00 回复：1 关注量：163

在基因组中存在着大量的重复序列，根据其重复的程度可分为简单重复序列、中度重复序列和高度重复序列。简单重复序列(Simple Sequence Repeat，SSR)在真核生物基因组中广泛存在，一般是以1-6bp组成较低程度的重复序列，主要以2-3个核苷酸为重复单位如(GA)n、(AC)n和(GAA)n等。从进化角度看物种间重复序列的差异是自然选择的结果。因此鉴定SSR在基因组分析中有重要意义。

今天给大家推荐一款鉴定简单重复序列的软件MISA（MIcroSAtellite identification tool）。MISA是一个用perl语言写的一个从fasta序列中鉴定SSR的脚本。

该软件下载地址：http://pgrc.ipk-gatersleben.de/misa/

下面是软件的附带的使用说明。

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DESCRIPTION: Tool for the identification and localization of
(I)perfect microsatellites as well as
(II) compound microsatellites (two individual microsatellites,
disrupted by a certain number of bases)
SYNTAX: misa.pl
Single file in FASTA format containing the sequence(s).
In order to specify the search criteria, an additional file containing
the microsatellite search parameters is required named "misa.ini", which
has the following structure:
(a) Following a text string beginning with 'def', pairs of numbers are
expected, whereas the first number defines the unit size and the
second number the lower threshold of repeats for that specific unit.
(b) Following a text string beginning with 'int' a single number defines
the maximal number of bases between two adjacent microsatellites in
order to specify the compound microsatellite type.
Example:
definition(unit_size,min_repeats):1-10 2-6 3-5 4-5 5-5 6-5
interruptions(max_difference_for_2_SSRs): 100
EXAMPLE: misa.pl seqs.fasta

运行MISA时还需要另外一个文件，misa.ini。该文件记录鉴定的SSR的参数。默认情况下：

第一行：definition(unit_size,min_repeats) 是SSR pattern

第二行：interruptions(max_difference_for_2_SSRs)是两个SSR之间的间隔。

筛选标准为:单核苷酸重复的次数在16次或 16次以上 ,二核苷酸重复的次数在 6次或 6次以上 ,三至六核苷酸重复的次数在 5次或 5次以上等。同时 ,也筛选中间被少数碱基 (间隔小于100或等于100)打断的 ( interrupted)不完全重复的SSR）

运行前将misa.ini与misa.pl 放在一起，输入的序列存在fasta文件里面，然后运行下面的命令：

1	perl misa.pl genome.fasta

利用MISA鉴定简单重复序列(SSR)

楼主 | 收藏 | 举报 2018-10-04 00:00 浏览: 163 回复: 1

今天给大家推荐一款鉴定简单重复序列的软件MISA（MIcroSAtellite identification tool）。MISA是一个用perl语言写的一个从fasta序列中鉴定SSR的脚本。

该软件下载地址：http://pgrc.ipk-gatersleben.de/misa/

下面是软件的附带的使用说明。

1
2
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DESCRIPTION: Tool for the identification and localization of
(I)perfect microsatellites as well as
(II) compound microsatellites (two individual microsatellites,
disrupted by a certain number of bases)
SYNTAX: misa.pl
Single file in FASTA format containing the sequence(s).
In order to specify the search criteria, an additional file containing
the microsatellite search parameters is required named "misa.ini", which
has the following structure:
(a) Following a text string beginning with 'def', pairs of numbers are
expected, whereas the first number defines the unit size and the
second number the lower threshold of repeats for that specific unit.
(b) Following a text string beginning with 'int' a single number defines
the maximal number of bases between two adjacent microsatellites in
order to specify the compound microsatellite type.
Example:
definition(unit_size,min_repeats):1-10 2-6 3-5 4-5 5-5 6-5
interruptions(max_difference_for_2_SSRs): 100
EXAMPLE: misa.pl seqs.fasta

运行MISA时还需要另外一个文件，misa.ini。该文件记录鉴定的SSR的参数。默认情况下：

第一行：definition(unit_size,min_repeats) 是SSR pattern

第二行：interruptions(max_difference_for_2_SSRs)是两个SSR之间的间隔。

运行前将misa.ini与misa.pl 放在一起，输入的序列存在fasta文件里面，然后运行下面的命令：

1	perl misa.pl genome.fasta

楼主 | 收藏 | 举报 2018-10-04 00:00 浏览: 163 回复: 1

今天给大家推荐一款鉴定简单重复序列的软件MISA（MIcroSAtellite identification tool）。MISA是一个用perl语言写的一个从fasta序列中鉴定SSR的脚本。

该软件下载地址：http://pgrc.ipk-gatersleben.de/misa/

下面是软件的附带的使用说明。

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
DESCRIPTION: Tool for the identification and localization of
(I)perfect microsatellites as well as
(II) compound microsatellites (two individual microsatellites,
disrupted by a certain number of bases)
SYNTAX: misa.pl
Single file in FASTA format containing the sequence(s).
In order to specify the search criteria, an additional file containing
the microsatellite search parameters is required named "misa.ini", which
has the following structure:
(a) Following a text string beginning with 'def', pairs of numbers are
expected, whereas the first number defines the unit size and the
second number the lower threshold of repeats for that specific unit.
(b) Following a text string beginning with 'int' a single number defines
the maximal number of bases between two adjacent microsatellites in
order to specify the compound microsatellite type.
Example:
definition(unit_size,min_repeats):1-10 2-6 3-5 4-5 5-5 6-5
interruptions(max_difference_for_2_SSRs): 100
EXAMPLE: misa.pl seqs.fasta