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CompBioBench item

enriched-motif-identification-q1

Question

Consider the DNA sequence provided as dna_with_secret_motif.fasta. Of these motifs, which is the most prevalent? FOXA1, GATA3, MAX, STAT1, OCT4, P53, NANOG, HNF4A, TBP, FOS, MYC, JUN, FOXO1, CTCF, TCF7, SOX2, E2F1, CREB1, GATA1, KLF3.

Predicted answer
CTCFMost likely answer for this question; not uniquely determined from submitted scores.
Domain
Epigenomics
Question style
Synthetic/Augmented Data

An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.

Galaxy

12/12 terminal item results

UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches predictionUDT-only
AnswerCTCF
Workflow
Motif prevalence JASPAR 2026Motif prevalence JASPAR 2026 pvalue
Codex GPT-5.5

Replicate 2

Matches predictionUDT + standard tools
AnswerCTCF
Workflow
Scan candidate motifs with JASPAR 2026Scan candidate motifs with JASPAR 2026 v2Meme FimoDatamash OpsGrep
Total tokens
1.9M
Output
14.9K
Codex GPT-5.5

Replicate 3

Matches predictionUDT + standard tools
AnswerCTCF
Workflow
Motif prevalence with FIMOMotif prevalence with FIMO v2UDT render probeUDT render probe 2Meme Meme2 more tools
Total tokens
2.4M
Output
17.3K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionUDT-only
AnswerCTCF
Workflow
JASPAR FIMO candidate motif prevalence
Total tokens
813.5K
Output
7.3K
Codex GPT-5.6 Sol

Replicate 2

Matches predictionUDT + standard tools
AnswerCTCF
Workflow
Meme MemeJASPAR Candidate Motif InventoryScan Listed JASPAR Motifs and Rank Prevalence
Total tokens
1.7M
Output
10.2K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionUDT + standard tools
AnswerCTCF
Workflow
Meme MemeJASPAR Candidate Motif InventoryExtract JASPAR Candidate MotifsMeme FimoTF Motif Prevalence Summary JASPAR2026
Total tokens
3.6M
Output
11.7K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionStandard tools only
AnswerCTCF
Workflow
Meme Fimo
Total tokens
2.5M
Output
23.7K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
AnswerCTCF
Workflow
Meryl Count KmersMeryl PrintMeme FimoSelect columnsCount1
Total tokens
5.4M
Output
26.1K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionStandard tools only
AnswerCTCF
Workflow
Meme FimoCount1Select columns
Total tokens
2.8M
Output
18.5K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionStandard tools only
AnswerCTCF
Workflow
Meme MemeMeme Fimo
Total tokens
9.8M
Output
29.2K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionStandard tools only
AnswerCTCF
Workflow
Meme MemeEmboss: Fuzznuc37
Total tokens
3.8M
Output
16.8K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionStandard tools only
AnswerCTCF
Workflow
Meme MemeFasta Regex FinderCount1
Total tokens
5.0M
Output
21.2K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
AnswerCTCF
Workflow
Local codePython
Codex GPT-5.5

Replicate 2

Matches prediction
AnswerCTCF
Workflow
Local codePython
Codex GPT-5.5

Replicate 3

Matches prediction
AnswerCTCF
Workflow
Local codePython

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
AnswerCTCF
Workflow
Local code
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
AnswerCTCF
Workflow
Local code
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
AnswerCTCF
Workflow
Local codePython

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
AnswerCTCF
Workflow
Local codePython
Total tokens
367.5K
Output
7.2K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
AnswerCTCF
Workflow
Local codePython
Total tokens
336.0K
Output
8.9K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
AnswerCTCF
Workflow
Local codePython
Total tokens
2.3M
Output
19.4K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
AnswerCTCF
Workflow
Local code
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
AnswerCTCF
Workflow
Local codePython
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
AnswerCTCF
Workflow
Local code

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
AnswerCTCF
Workflow
Local codePythonSciPy
Total tokens
88.2K
Output
1.3K