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SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns 1.0.9753.40023.
01 Namespaces
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns
| Type | Summary | Members |
|---|---|---|
| LociExtensions | 将序列特征的搜索结果转换为SimpleSegment对象类型 | 3 |
| LociFilter | 3 | |
| MotifLog | Simple site information of the TF motif site. | 3 |
| SSRSearch | 微卫星DNA：重复单位序列最短，只有2～6bp，串联成簇，长度50～100bp，又称为短串联重复序列（Short Tandem Repeat STR)。 广泛分布于基因组中。 其中富含A-T碱基对，是在研究DNA多态性标记过程中发现的。1981年Miesfeld等首次发现微卫星DNA， 其重复单位长度一般为1～6个核苷酸，双核苷酸重复单位常为(CA)n和… | 4 |
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.DNAOrigami
| Type | Summary | Members |
|---|---|---|
| Project | 3 | |
| ScaffoldOrthogonality | evaluate scaffold orthogonality This script analyses orthogonality of two DNA-Origami scaffold strands. | 1 |
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.LociFilter
| Type | Summary | Members |
|---|---|---|
| Compares | 4 |
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Motif
| Type | Summary | Members |
|---|---|---|
| MotifPattern | Regular expression model for the motifs | 6 |
| PWM | Build probability matrix from clustal multiple sequence alignment. | 2 |
| ResidueSite | A column in the motif | 10 |
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Pattern
| Type | Summary | Members |
|---|---|---|
| PatternSearch | 使用用户指定的正则表达式搜索指定的序列数据 | 1 |
| SegLoci | 程序所搜索到的一个序列片段 | 3 |
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically
| Type | Summary | Members |
|---|---|---|
| Analysis | 2 | |
| Imperfect | 在互补链部分的回文，由于Mirror其实就是简单重复序列，所以在这里不再编写了 | 2 |
| ImperfectPalindrome | 只有一部分的序列是匹配上的回文序列 | 9 |
| MirrorPalindrome | 种子片段在正向链找得到自己的反向片段，即为镜像回文片段 | 3 |
| Palindrome | === Palindromic hexamers === For a given sequence, any palindrome of 6 nt (e.g., AAATTT) Is given a value of 1, while all bases Not included inpalindromic hexamers are given a v… | 7 |
| PalindromeLoci | Mirror 或者 Palindrome 位点的搜索结果的csv文件存储模型 | 7 |
| PalindromeSearch | 片段在反向链找得到自己的反向片段 | 2 |
| Repeats | The sequence segment of the nucleotide repeats.(重复的核酸片段) | 4 |
| RepeatsSearchAPI | 4 | |
| RepeatsSearcher | 2 | |
| RepeatsView | 正向重复位点的序列模型 | 3 |
| ReversedRepeatSeacher | 2 | |
| ReverseRepeats | The reversed repeats.(反向重复序列) | 2 |
| ReverseRepeatsView | 反向重复序列的模型，继承于RepeatsView模型 | 2 |
| SearchWorker | 2 |
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.Seeding
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.SimilarityMatches
| Type | Summary | Members |
|---|---|---|
| FuzzyMirrors | 1 | |
| LociMatchedResult | 4 | |
| MirrorPalindrome | 模糊相等的 | 2 |
| Repeats | 模糊匹配重复的序列片段 | 4 |
| ReversedLociMatchedResult | 2 |