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To perform a motif search please upload or paste your sequence at the text area provided. Select the type of input, type in the motif(s) to search for at the box provided and press the send button.

Motif Search

Help: Use the Simplified Motif Search Mode to search for up to two motifs separated by a comma. In this option the program will accept motif sequences bearing only nucleotide and amino acid codes (for the protein motif search "x" is also allowed). In the Advance Motif Search Mode ver.2 the user can search for any number of motifs separated with a dash "-". Also regex quantifiers (?, *, [, ], {, }, +), numbers and IUB codes are allowed to build the motif(s) of interest. Click at the [See examples] option at the bottom of each box for further information.
Notice: In the sequence upload area any numbers, spaces, star (*) and brackets (){}[] will be ignored.

Uploading sequence from txt file: Upload your file with your sequence. Only TXT files will be accepted. AFTER define the type of input (DNA, RNA or Protein) at the desired search mode box (Simple or Advanced), type in the motif(s) to search for and press the Send button. The uploaded sequence can be also edited while being in the text box. Any sequence already present in the text box prior the upload will be replaced from the uploaded one.

Simplified motif search mode

Please select type of input:

: DNA sequence;    : RNA sequence;    : Protein sequence;   

Insert below up to two motifs separated by a comma "," :

Use this form to search for up to two motif sequences without the use of wild card characters.
[See examples]

Advanced motif search mode ver.2

Please select type of input:

: DNA sequence;    : RNA sequence;    : Protein sequence;  

Insert below motif(s) to search for separated by a dash "-" :

Use this form to run advanced motif searches using wild card characters.
[See examples]

Enter your sequence:


*The IUB ambiguity codes are : R = (G or A), Y = (C or T), M = (A or C), K = (G or T), S = (G or C), W = (A or T), B = (C or G or T), D = (A or G or T), H = (A or C or T), V = (A or C or G), N = (A or C or G or T)*

When you use this bioinformatics applet please cite this paper.

Created together with Dr. D. Kaloudas. For any comments or inquires you can email him...