MEME_TEXT

Full name SMRUCC.genomics.Interops.NBCR.MEME_Suite.DocumentFormat.MEME.Text.MEME_TEXT Assembly SMRUCC.genomics.Interops.NBCR.MEME_Suite.Documents Members 9

MEME - Motif discovery tool

00 Remarks

MEME - Motif discovery tool

MEME version 3.5.4 (Release date: 3.5.4)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net.

REFERENCE

If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.

01 Syntax

SMRUCC.genomics.Interops.NBCR.MEME_Suite.DocumentFormat.MEME.Text.MEME_TEXT

02 Methods

Name	Overloads	Summary
Load	1	Load the motif data from the meme text format calculation result
GetLength	1	函数自动从meme.text文档里面解析出序列数据源的长度参数，假若你不太方便手工输入序列长度的话
SafelyLoad	1	发生错误会返回空值
__createBlockDiagrams	1	可能会有完全一样的出现
__tryParseMotif	1	MOTIF 1 width = 21 sites = 12 llr = 178 E-value = 4.6e-004
Statics	1
Normalization	1	计算单位段长度之内的motif出现的频率的高低 if the maximum density value is too small(This is mainly caused by the long genome sequence length but fewer number of the motifs, so the density maybe t…
DistanceNormalization	1	计算基因组之间的距离，使用这个文件之中的数据利用飞利浦软件里面的Distance matrix methods方法进行进化树的构建
ExportMotif	1

03 Members

method Load #

Load(String, Boolean)

Load the motif data from the meme text format calculation result

Parameters

Name	Type	Description
`path`	`String`	-

Returns

Load the motif data from the meme text format calculation result output file.

method GetLength #

GetLength(String)

函数自动从meme.text文档里面解析出序列数据源的长度参数，假若你不太方便手工输入序列长度的话

Parameters

Name	Type	Description
`path`	`String`	-

method SafelyLoad #

SafelyLoad(String, Boolean)

发生错误会返回空值

Parameters

Name	Type	Description
`path`	`String`	-

method __createBlockDiagrams #

__createBlockDiagrams(String())

可能会有完全一样的出现

Parameters

Name	Type	Description
`str`	`String()`	-

method __tryParseMotif #

__tryParseMotif(String, String)

MOTIF 1 width = 21 sites = 12 llr = 178 E-value = 4.6e-004

Parameters

Name	Type	Description
`strData`	`String`	-

method Statics #

Statics(IEnumerable(Of Motif), Func(Of String, String))

Remarks

motif1 motif2 motif3 genome1 genome2 genome3

Parameters

Name	Type	Description
`Motifs`	`IEnumerable(Of Motif)`	-
`getsId`	`Func(Of String, String)`	获取基因组编号的函数指针

method Normalization #

Normalization(File, String, Int32)

计算单位段长度之内的motif出现的频率的高低

if the maximum density value is too small(This is mainly caused by the long genome sequence length but fewer number of the motifs, so the density maybe two small.), then you can using the scale(>0) parameter to adjust.

Remarks

可以使用本方法所生成的矩阵进行Gene Frequencies and Continuous Character Data Programs的方法进行进化树的绘制

phylip软件之中的帮助说明

The programs in this group use gene frequencies and quantitative character values. One (Contml) constructs maximum likelihood estimates of the phylogeny, another (Gendist) computes genetic distances for use in the distance matrix programs, and the third (Contrast) examines correlation of traits as they evolve along a given phylogeny.

When the gene frequencies data are used in Contml or Gendist, this involves the following assumptions:

Different lineages evolve independently. After two lineages split, their characters change independently. Each gene frequency changes by genetic drift, with or without mutation (this varies from method to method). Different loci or characters drift independently. How these assumptions affect the methods will be seen in my papers on inference of phylogenies from gene frequency and continuous character data (Felsenstein, 1973b, 1981c, 1985c).

Parameters

Name	Type	Description
`csv`	`File`	-
`faDIR`	`String`	-
`scale`	`Int32`	-1表示使用自动配置的scale参数，其他的非零的正数则表示指定扩大的级别

method DistanceNormalization #

DistanceNormalization(File, String, String)

计算基因组之间的距离，使用这个文件之中的数据利用飞利浦软件里面的Distance matrix methods方法进行进化树的构建

Parameters

Name	Type	Description
`csv`	`File`	-
`faDIR`	`String`	-
`queryref`	`String`	参照的基因组的编号

method ExportMotif #

ExportMotif(String)

Parameters

Name	Type	Description
`MEME_Text`	`String`	MEME text motif 文档的文件路径