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Introduction

This web tool enables plant biologists to search for DNA motifs in the proximal promoters, and 3' untranslated regions of all genes from 50 genome-sequenced plant species. The motifs can be in the format of either degenerate sequences or Position Probability Matrix (PPM).

The options to do motif search include:

(1) Search Motif(s) in Your Own Sequence(s) : Enter a number of motifs and any target sequences of your own to search.

(2) Search Motif(s) in the Flanking Sequence of Genes in one of the 50 Plant Species : Enter a number of motifs and a list of gene IDs to search.
    (The same transcript gene IDs from Phytozome are used)

For additional information, please refer to our publication.
http://plantmethods.biomedcentral.com/articles/10.1186/s13007-016-0126-6

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1. Search Motif(s) in Your Own Sequence(s)

-- Exact search


- or -
Click here to select from available motifs

- or - paste the motifs in fasta format

- or - paste the target sequence in fasta format



Sample target sequence file : CEL478.fasta.txt
Sample target sequence file(Large) : Athaliana_all_genes_2000bp.fasta.txt
Sample motif file : motif_100.fasta.txt
Sample output file : CEL478.fasta_exact_match.csv

2. Search Motif(s) in the Flanking Sequence of Genes in one of the 50 Plant Species

-- Exact search or matrix search

   One or mulitple motifs should be submitted in the same file in Fasta or PPM format (see examples)

  Sample motif input file : motif_100.fasta.txt |  matrix.ppm.txt
  Sample output file : (Large file) Athaliana_all_genes_2000bp_100Motif_exact_match.csv | myfiles.zip


- or -
Click here to select from available motifs
- or - paste the motifs in fasta format



  If needed, download the annotation file to extract the gene IDs (Right Click > Save As..) :

   To search all the genes of the selected species check here 







  Please double check all input files before submitting to the ExactSearch

How to cite?

Gunasekara, C. A. Subramanian, Avvari, R. K., B. Li, Chen, S. and H. Wei. 2016. ExactSearch: A web-based plant motif search tool. Plant Methods 12:26 10.1186/s13007-016-0126-6

To read more:
Plant Methods

Email: cjgunase@mtu.edu, hairong@mtu.edu
School of Forest Resources and Environmental Science, Michigan Technological University
Last Update:05/23/2016
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