The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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DREME 5.0.5

DREME (Discriminative Regular Expression Motif Elicitation) finds relatively short motifs (up to 8 bases) fast, and can perform discriminative motif discovery if given a negative set, consisting of sequences unlikely to contain a motif of interest that is however likely to be found in the main ("positive") sequence set. If you do not provide a negative set the program shuffles the positive set to provide a background (in the role of the negative set).

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Quick Start

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> iplant_training -> advanced_chip-seq

Input File(s)

Use fastaFromBed_out.fa from the directory path  Community Data -> iplantcollaborative -> iplant_training -> advanced_chip-seq -> 03_best_summits_slop100_fastaFromBed as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect several files as output. For the test case, the output files are located in the directory Community Data -> iplantcollaborative -> iplant_training -> advanced_chip-seq -> dreme -> dreme_out .

Tool Source for App

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1 Comment

  1. ★★★★★ null (by scyxr)