ESEfinder



Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang and Adrian R. Krainer




With release 2.0, ESEfinder allows to directly display the output graphically


- the analyzed (exonic) sequence is reproduced along the X-axis.
  
Either the actual nucleotides or the nucleotide number can be displayed

- only the high-score values (the values above the selected threshold) are represented

- the heigth of the bars represents the motif scores

- the width of the bars indicates the length of the motif (6, 7 or 8 nucleotides)

- the different SR protein high-scores are color-coded as illustrated below


EXAMPLE:

Sequence ID: Seq#1 BRCA1 WT
Sequence:
ATGCTGAGTTTGTGTGTGAACGGACACTGAAATATTTTCTAGGAATTGCG
GGAGGAAAATGGGTAGTTAGCTATTTCT

Length=78

Threshold applied

   display sequence from nt to nt

 

 X-Axis:           sequence nucleotide position

 
 SF2/ASF

 
 SC35

 
 SRp40

 
 SRp55

 Thr=1.956

 Thr=2.383

 Thr=2.67

 Thr=2.676




web site created and mantained by Luca Cartegni (cartegni@cshl.edu). CGI-scripts implemented by Jinhua Wang (wang@cshl.edu)

 

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Krainer's lab page

Zhang's lab page