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CompBioBench item

orf-annot-q1

Question

You are given a fasta file containing a human mRNA sequence. Find the main CDS of the sequence, return the start position of the CDS (in a 0-based coordinate system, starting from the first base of the given sequence) and the length of the translated protein in the format 4;2.

Predicted answer
282;351Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Genomics
Question style
Retrieval

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 predictionStandard tools only
Answer282;351
Workflow
Emboss: Getorf42Fasta Compute Length
Total tokens
461.9K
Output
4.0K
Codex GPT-5.5

Replicate 2

Matches predictionUDT + standard tools
Answer282;351
Workflow
Emboss: Getorf42Find main CDS from FASTAFasta Compute Length
Total tokens
429.8K
Output
5.6K
Codex GPT-5.5

Replicate 3

Matches predictionStandard tools only
Answer282;351
Workflow
Emboss: Getorf42Fasta Compute Length
Total tokens
156.3K
Output
3.1K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionStandard tools only
Answer282;351
Workflow
OrfipyCshl Fasta Nucleotides ChangerFasta Compute Length
Codex GPT-5.6 Sol

Replicate 2

Matches predictionStandard tools only
Answer282;351
Workflow
OrfipyCshl Fasta Nucleotides ChangerBedtools GetfastabedSeqkit TranslateFasta Compute Length
Total tokens
1.3M
Output
4.7K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionStandard tools only
Answer282;351
Workflow
Emboss: Getorf42Fasta Compute Length
Total tokens
311.4K
Output
2.2K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionStandard tools only
Answer282;351
Workflow
Emboss: Getorf42Fasta Compute Length
Total tokens
297.5K
Output
6.9K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
Answer282;351
Workflow
Cshl Fasta Nucleotides ChangerOrfipyFasta Compute Length
Total tokens
439.6K
Output
8.4K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionStandard tools only
Answer282;351
Workflow
Emboss: Getorf42
Total tokens
172.2K
Output
4.5K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionStandard tools only
Answer282;351
Workflow
Emboss: Getorf42Fasta Compute Length
Total tokens
576.5K
Output
6.0K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionStandard tools only
Answer282;351
Workflow
Emboss: Getorf42Fasta Compute LengthEmboss: Extractseq35Orfipy
Total tokens
1.5M
Output
8.9K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionStandard tools only
Answer282;351
Workflow
TransdecoderCshl Fasta Nucleotides ChangerEmboss: Getorf42Fasta Compute LengthBg Find Subsequences1 more tools
Total tokens
1.1M
Output
9.6K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
Answer282;351
Workflow
Local code
Codex GPT-5.5

Replicate 2

Matches prediction
Answer282;351
Workflow
Local codePython
Codex GPT-5.5

Replicate 3

Matches prediction
Answer282;351
Workflow
Local codePythonBLASTN

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
Answer282;351
Workflow
Local code
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
Answer282;351
Workflow
Local codePython
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
Answer282;351
Workflow
Local codePython

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
Answer282;351
Workflow
Local codePython
Total tokens
51.3K
Output
2.5K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
Answer282;351
Workflow
Local codePython
Total tokens
151.9K
Output
5.1K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
Answer282;351
Workflow
Local codePython
Total tokens
101.8K
Output
4.1K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
Answer282;351
Workflow
Local code
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
Answer282;351
Workflow
Local codePython
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
Answer282;351
Workflow
Local code

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
Answer282;351
Workflow
Local codePython
Total tokens
47.0K
Output
373