ATGC Platform

DExTER Completed

Job name

Example

Job ID

71cb194e-4dc4-4b4d-aca7-f153659cd340

Created

2026-04-27 16:32

Expires

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Command executed

apptainer run dexter.sif -fasta_file ATGminus2000plus2000.fasta -expression_file Otto_newID.csv -target_condition 0h -experience_directory experience -nb_thread 8 -alignement_point_index 2000 -nb_bins 13 -kmer_max_length 0 -random_seed 686185200 -correlation_increase 0.01 -correlation_increase_ratio 0.1 -correlation_min 0.0 -log_transform -uniform_bins -verbose -no_progress -final_lasso
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Acknowledgements

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Suggested acknowledgement

Analyses were performed using the ATGC platform hosted by LIRMM, University of Montpellier, CNRS.

Suggested citation for DExTER

  • DExTER: Menichelli C, Guitard V, Martins RM, Lebre S, Lopez-Rubio JJ, Lecellier CH, Brehelin L. Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes. PLoS Computational Biology. 2021;17(4):e1008909. doi:10.1371/journal.pcbi.1008909

Exploration Graph

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Legend

Expansion Control Segmentation Other

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DExTER Outputs

Execution log

Download (output.log) 
==============================
[2026-04-27T16:32:26+00:00] Pre-processing inputs for DExTER (job: 71cb194e-4dc4-4b4d-aca7-f153659cd340)
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| DExTER - Christophe Menichelli, Vincent Guitard, Sophie Lèbre, Jose-Juan Lopez-Rubio, Charles-Henri Lecellier, Laurent Bréhélin (2020) |
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contact: christophe.menichelli@lirmm.fr & laurent.brehelin@lirmm.fr

Processing arguments...
Testing requirements...
Clearing directories...
Generating sequences sets...
Using 3487 sequences in training set and 1744 sequences in testing set.
Extract expression data...

100%|██████████| 5232/5232 [00:00<00:00, 259637.94seq/s]
Running pre-load procedure...

0it [00:00, ?it/s]
221143it [00:00, 2211426.84it/s]
355708it [00:00, 2216317.67it/s]

100%|██████████| 16/16 [00:27<00:00,  1.74s/it]
Exploring...
Initialization of the broker...

Generation LASSO matrices...
 -> ALL domains

100%|██████████| 81/81 [00:18<00:00,  4.32it/s]

100%|██████████| 81/81 [00:13<00:00,  6.11it/s]

Computing LASSO...
.LASSO on ALL domains
-> nb_iter = 156
-> Cor = 0.6970084495644036
-> (-0.07 * %AT.-1332_-1) + (-1.78 * %TAAA.1_333) + (-0.14 * %AA.334_666) + (-0.1 * %AA.1666_1998) + (4.77 * %TGG.1_333) + (-0.18 * %AA.1000_1332) + (0.15 * %AA.1_333) + (0.02 * %TT.-2000_2000) + (-5.56 * %TC.-2000_2000) + (-0.63 * %AAA.334_666) + (2.0 * %TTT.-1665_666) + (-0.65 * %AAT.1666_1998) + (-0.46 * %AAA.1_333) + (3.88 * %AG.0_666) + (0.01 * %GG.1_333) + (-3.65 * %AAT.1000_1998) + (1.33 * %AG.667_999) + (-13.58 * %CG.-2000_2000) + (-9.06 * %AC.-1332_-1) + (3.68 * %TAT.-1332_-1) + (-0.01 * %TAA.1000_1332) + (17.19 * %CC.-2000_2000) + (0.73 * %AGA.667_999) + (1.25 * %TAAA.1_1998) + (-5.15 * %AG.-1332_-334) + (-4.91 * %TC.-1332_333) + (-2.51 * %AGG.667_999) + (1.13 * %AA.-2000_2000) + (3.8 * %AGT.0_666) + (0.17 * %AG.-2000_-1333) + (9.51 * %GC.-2000_2000) + (1.04 * %GA.-2000_-1666) + (-8.19 * %ATAAA.1_1998) + (2.14 * %AAAAA.-1998_-1) + (1.45 * %GG.-1665_-1333) + (-5.28 * %CT.-1332_-1) + (1.46 *

...[truncated]...

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