The new downloadable version of Trawler is available here

Trawler is a integrated pipeline for the analysis of large scale chromatin-immunoprecipitation (ChIP) data maintained by the Ettwiller 's lab.

Click here for the ChIP-chip publically available and analysed using Trawler.

The stand alone version of Trawler will be available shortly

Before using trawler please read the documentation.
See example here. This example corresponds to the chromatin IP from Ren et al.
You can also test Trawler using examples of sample sequences.


[1] The sequences
Sequences should be repeat masked and upper case letter (ATCG)

Background sequences file
(in fasta format)



OR

choose a background from the list of precomputed backgrounds (precomputed background are repeat masked)

Sample sequences file
(in fasta format); see example here



If you have ensembl gene IDs you can automatically obtain the sequences here.


[2] Ortholog sequences (OPTIONAL)

Orthologous sequences
(in fasta format); see an example here



Sorted according to :


If you have ensembl IDs in one species you can automatically obtain the orthologous sequences here.


[3] Parameters (OPTIONAL)
These default parameters work well with most of the ChIP-ChIP data
(please read the documentation before changing them)

Minimum number of motif occurence in sample (info) This is an important parameter. (for example 10)
Please check the documentation.
Maximum number of mismatches (info) This parameter allow for more of less degeneracy in the motif description (for example 2)
Minimum motif length (info) for example 6 bp
Clustering procedures (info) This parameters is used for the clustering of the different family found.


[4] Trawler output (OPTIONAL)

output format :

If the whole analysis option is selected, the complete analysis is done (including clustering and mapping back the motif to the sequence or alignments (if orthologous sequences are provided).

If the over-representation only option is selected, then the output of trawler is a list of motifs that are over-represented in the sample.

[5] Your email address

email : An email containing a link to your result will be send to you




The typical running time is around one to two minute(s)
(if you are using the default parameters and your sample size is around 1 Mb)

Please be patient (do not click multiple times)


Any questions or comments email :

Laurence Ettwiller   ettwille{at}embl.de
Mirana Ramialison   ramialis{at}embl.de
or Benedict Paten   paten{at}ebi.ac.uk

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