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Chapter 14
General sequence analyses
Contents
14.1 Shuffle sequence . . . . . . . . . . . . . . . . .
14.2 Dot plots . . . . . . . . . . . . . . . . . . . . . .
14.2.1 Create dot plots . . . . . . . . . . . . . . .
14.2.2 View dot plots . . . . . . . . . . . . . . . .
14.2.3 Bioinformatics explained: Dot plots . . . . .
14.2.4 Bioinformatics explained: Scoring matrices
14.3 Local complexity plot . . . . . . . . . . . . . . .
14.4 Sequence statistics . . . . . . . . . . . . . . . .
14.4.1 Bioinformatics explained: Protein statistics
14.5 Join sequences . . . . . . . . . . . . . . . . . .
14.6 Pattern Discovery . . . . . . . . . . . . . . . . .
14.6.1 Pattern discovery search parameters . . . .
14.6.2 Pattern search output . . . . . . . . . . . .
14.7 Motif Search . . . . . . . . . . . . . . . . . . . .
14.7.1 Dynamic motifs . . . . . . . . . . . . . . .
14.7.2 Motif search from the Toolbox . . . . . . .
14.7.3 Java regular expressions . . . . . . . . . .
14.7.4 Create motif list . . . . . . . . . . . . . . .
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CLC Protein Workbench offers different kinds of sequence analyses, which apply to both protein
and DNA. The analyses are described in this chapter.
14.1
Shuffle sequence
In some cases, it is beneficial to shuffle a sequence. This is an option in the Toolbox menu under
General Sequence Analyses. It is normally used for statistical analyses, e.g. when comparing an
alignment score with the distribution of scores of shuffled sequences.
Shuffling a sequence removes all annotations that relate to the residues.
select sequence | Toolbox in the Menu Bar | General Sequence Analyses (
Shuffle Sequence ( )
195
) |