PromAn
, integrated and knowledge-based promoter analysis
Please enter your
personal email
as a link to the results file will be provided by mail.
Important recommandations:
Promoter sequences must not be longer than
20 kb
. Sequences (promoter, pattern and PFM) have to be in
fasta format
.
Genomic sequences
The
HomoloGene
database can be used to define and extract promoter sequences ("Download" link).
Reference
genomic sequence
Orthologous
genomic sequence(s)
Example
(Mouse rhodopsin)
Example
(Mouse rhodopsin orthologs)
or
PromAn options
1-
Transcription Start Site
(
TSS
) location on the query promoter sequence
DBTSS v5.2.0 (2006)
:
Yes
No
EPD v87
:
Yes
No
FirstEF
:
Yes
No
Eponine
:
Yes
No
GenScan
:
Yes
No
2-
Transcription Factor Binding Sites
(
TFBS
) prediction
2.1-
User-defined
TFBS search
Patterns
:
IUPAC nucleic acid code
in
fasta format
.
Position Frequency Matrices
(
PFMs
)
Example
(TATA_Box, CCAAT_Box)
Example
(TATA_Box, CCAAT_Box)
2.2- Public
TRANSFAC v7.0 (2005)
database
Nucleotide distribution matrices:
MinFN
MinFNGood
MinFP
MinFPGood
MinSum
MinSumGood
None
Cell cycle:
Yes
No
Liver:
Yes
No
Immune cell:
Yes
No
Muscle:
Yes
No
2.3-
JASPAR (2006)
database
JASPAR CORE:
Yes
No
JASPAR FAM:
Yes
No
JASPAR phyloFACTS:
Yes
No
2.4-
Specific TFBS matrices
extracted from
bibliography
(2006)
Retina:
Yes
No
Nuclear receptors:
Yes
No
3-
Phylogenetic footprinting
: promoter conservation profiling
Method to align all the promoter sequences:
MultiZ
PromAn results provided by mail
1- PromAn
results file
with the ".PromAn" extension
You can download
here
the PromAn results file of the rhodopsin as example.
2-
PromAnGUI
interactive graphical user interface
You can download
here
the last version of PromAnGUI. The free
ActiveTcl distribution 8.4
is required for PromAnGUI. ActiveTcl 8.4.12 for windown is directly available
here
3-
Multiple alignment
of the genomic sequences in
fasta format
You can download
here
the multiple alignment provided by PromAn on the example of the rhodopsin.
Help
PromAn help
,
PromAnGUI help
,
PromAn history
.
If you have any problems or questions, please, feel free to contact us at
Laurent.Bianchetti@igbmc.u-strasbg.fr
