Cistome helps map cis-elements in Arabidopsis. Cistome incorporates 3rd party prediction programs that permit wobbles at positions within a putative cis-element. PSSMs (position-specific scoring matrices) as opposed to consensus sequences are returned, along with an evaluation of their significance, performed by Bootmer2. In addition, Cistome will display literature-documented cis-elements from PLACE.

If you find this tool useful, please cite: Ryan S. Austin, Shu Hiu, Jamie Waese, Matthew Ierullo, Asher Pasha, Nina Wang, Jim Fan, Curtis Foong, Robert Breit, Darrell Desveaux, Alan Moses, Nicholas J. Provart (manuscript in preparation), New BAR Tools for Mining Expression Data and Exploring Cis-Elements in Arabidopsis thaliana.

If you have any questions, please contact:

Nicholas Provart
Department of Cell and Systems Biology
University of Toronto

Input must be supplied in the following FASTA format as modelled after the PLACE DB. An annotation line beginning with a '>' symbol and label followed by a new line with the consensus sequence using any valid IUPAC nucleotide codes.

e.g:

> ABRE
RYACGTGT
> BZIP-core
ACGT
> RYREPEAT
CATGCA

Be sure to check the proper radio button before submitting the query.

Input must be supplied in the following FASTA like format. An annotation line beginning with a '>' symbol and label followed by a series of tab delimited lines providing the frequency of base pairs along the length of the motif. All columns should possess a common sum and all rows should possess a common number of elements as would be expected of a valid position specific scoring matrix. Rows values are represented below.

> label
A values
C values
G values
T values

e.g.
>ABRELATERD1
22   0    0    0    0   
0    22   0    0    0   
0    0    22   0    22
0    0    0    22   0   
>ABRERATCA
2    20   0    0    0    0    0 
18   0    20   0    3    0    1 
0    0    0    20   0    20   6 
0    0    0    0    17   0    13
>GTATERD1
55   0    0    0
0    55   0    0
0    0    55   0
0    0    0    55

Be sure to check the proper radio button before submitting the query.