id stringlengths 5 40 | track stringclasses 3
values | task_type stringlengths 9 32 | question stringlengths 76 630 | reference_answer stringlengths 167 1.33k | instruction stringclasses 1
value | model stringclasses 1
value | reasoning_effort stringclasses 1
value | previous_content stringlengths 46 520 | previous_reasoning stringlengths 110 1.8k | content stringlengths 191 712 | reasoning_content stringlengths 208 4.4k | finish_reason stringclasses 1
value | usage dict | source_dataset stringclasses 1
value | source_config stringclasses 1
value | source_revision stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
bisulfite_conversion_t1_0185 | computational | bisulfite_conversion | Below is a single-stranded DNA sequence written in the 5'-to-3' direction:
5'-TCTCTTCGGGGTTGGAAGCGACTTGCTTCATGAC-3'
In a bisulfite sequencing assay, unprotected cytosines are converted to thymines, while protected cytosines remain unchanged. Given that only the cytosines at 1-based positions 2, 4, 7, 22, and 29 are pr... | To solve this revision problem, I can walk through the bisulfite conversion step by step:
First, I note the biological principle: sodium bisulfite deaminates unmethylated (unprotected) cytosine residues into uracil, which is read as thymine during sequencing, whereas methylated (protected) cytosines resist this reacti... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | The resulting bisulfite-converted sequence is:
**5′-TCTCTTCGGGGTTGGAAGTGACTTGTTTCATGAT-3′** | We need transform C unprotected to T. Need carefully index. Sequence TCTCTTCGGGGTTGGAAGCGACTTGCTTCATGAC. Let's enumerate.
1 T
2 C protected
3 T
4 C prot
5 T
6 T
7 C prot
8 G
9 G
10 G
11 G
12 T
13 T
14 G
15 G
16 A
17 A
18 G
19 C unprotected
20 G
21 A
22 C prot
23 T
24 T
25 G
26 C unprot
27 T
28 T
29 C prot
30 A
31 T
32 ... | 1. The cytosines occur at positions **2, 4, 7, 19, 22, 26, 29, and 34**.
2. Positions **2, 4, 7, 22, and 29** are protected and remain **C**.
3. The unprotected cytosines at positions **19, 26, and 34** are converted to **T**.
The resulting sequence is:
**5'-TCTCTTCGGGGTTGGAAGTGACTTGTTTCATGAT-3'** | We need need carefully enumerate. Sequence length 36? Let's index. Given 5' T C T C T T C G G G G T T G G A A G C G A C T T G C T T C A T G A C
Let's count.
1 T
2 C
3 T
4 C
5 T
6 T
7 C
8 G
9 G
10 G
11 G
12 T
13 T
14 G
15 G
16 A
17 A
18 G
19 C
20 G
21 A
22 C
23 T
24 T
25 G
26 C
27 T
28 T
29 C
30 A
31 T
32 G
33 A
34 C. W... | stop | {
"completion_tokens": 700,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 570,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 570
},
"prompt_tokens": 263,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
bisulfite_conversion_t4_0398 | computational | bisulfite_conversion | Given the DNA sequence CTTTTCGTCCAACCACTATGTTGGCAACAACATCATTATTAAGCCA, apply bisulfite conversion using the following methylation rule: cytosines at 1-based positions 6, 9, 10, 13, 16, 25, 34, and 45 are protected and remain unchanged, while every unprotected C is converted to T. Report the resulting sequence in the 5'... | I apply the conversion in several steps.
First, I note that the protected cytosines are specified at 1-based positions 6, 9, 10, 13, 16, 25, 34, and 45.
Next, I scan the original sequence CTTTTCGTCCAACCACTATGTTGGCAACAACATCATTATTAAGCCA from left to right. Any C at one of the protected positions remains C.
I then conv... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | TTTTTCGTCCAACTACTATGTTGGCAATAATATCATTATTAAGTCA | We need carefully index. Need convert. Let's enumerate sequence.
CTTTTCGTCCAACCACTATGTTGGCAACAACATCATTATTAAGCCA
positions:
1 C protected? no (protected 6,9,10,13,16,25,34,45)
2 T
3 T
4 T
5 T
6 C protected
7 G
8 T
9 C prot
10 C prot
11 A
12 A
13 C prot
14 C unprotected ->T
15 A
16 C prot
17 T
18 A
19 T
20 G
21 T
22 T
2... | Step-by-step:
1. Keep the listed protected cytosines unchanged at positions 6, 9, 10, 13, 16, 25, 34, and 45.
2. Convert all other cytosines to thymine: positions 1, 14, 28, 31, and 44 become T.
3. Leave all non-cytosine bases unchanged and preserve the 5'-to-3' order.
Resulting sequence:
**TTTTTCGTCCAACTACTATGTTGGCA... | We need answer sequence after bisulfite conversion with specified protected Cs. Need compute carefully. Need use tool. Done. Now compute step-by-step inside tool.
We need convert DNA sequence CTTTTCGTCCAACCACTATGTTGGCAACAACATCATTATTAAGCCA length? Protected cytosines at 1-based positions 6,9,10,13,16,25,34,45 remain C.... | stop | {
"completion_tokens": 1842,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 1704,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 1704
},
"prompt_tokens": 251,
"p... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
crispr_activity_class_t3_0817 | computational | crispr_activity_class | Classify the expected SpCas9 activity for the guide–target pair below. A valid PAM has the form NGG. Guide positions 13–20 constitute the PAM-proximal seed, while positions 1–12 are PAM-distal. Choose from: Perfect match with valid PAM; Seed mismatch: strongly reduced; PAM-distal mismatch: mildly reduced or tolerated; ... | First, I check the PAM. CGG matches the required NGG pattern, so the PAM is valid.
Next, I compare the guide with the target. Their mismatch falls within positions 13–20, the PAM-proximal seed region.
Therefore, this guide–target pair is classified as having a seed mismatch, which is expected to strongly reduce SpCas... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | **Seed mismatch: strongly reduced.**
The target has a single mismatch at **guide position 14** (guide **T**, target **G**), which lies within the PAM-proximal seed region (positions 13–20). The PAM **CGG** is valid, but seed mismatches typically strongly reduce SpCas9 cutting. | We need compare 20nt. Guide TTT CAT TCA AGA TTC TTC AG. Target TTT CAT TCA AGA TGC TTC AG. mismatch positions? Let's index:
Guide 1 T 2T3T4C5A6T7T8C9A10A11G12A13T14T15C16T17T18C19A20G
Target: T T T C A T T C A A G A T G C T T C A G. position14 mismatch T->G. Seed 13-20, so strongly reduced. PAM CGG valid. Need choose o... | Step 1: Check the PAM. The PAM is CGG, which fits NGG (N = C followed by GG), so the PAM is valid.
Step 2: Align guide and target:
- Guide: TTTCATTCAAGA T TCTTCAG
- Target: TTTCATTCAAGA G CTTCAG
The only difference is at guide position 14: T in the guide vs G in the target.
Step 3: Locate the mismatch. Positions 13... | The user wants me to classify SpCas9 activity for a guide-target pair.
Guide: TTTCATTCAAGATTCTTCAG (20 nt)
Target: TTTCATTCAAGATGCTTCAG
PAM: CGG
Let me align them:
Guide: T T T C A T T C A A G A T T C T T C A G
Target: T T T C A T T C A A G A T G C T T C A G
Position numbering 1-20 from 5' end (PAM-distal is 1-12, ... | stop | {
"completion_tokens": 937,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 761,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 761
},
"prompt_tokens": 270,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
first_atg_frame_t5_0969 | computational | first_atg_frame | For the DNA sequence CCGGCTATGCAATGAGGCTTTTGCCAAGCGTAAAGAATAGATCCTA, identify the reading frame containing the first ATG. Number the reading frames +1, +2, and +3 starting from the first base. | I first scan the sequence from the 5′ end to locate the earliest ATG.
The first ATG starts at position 7 using 1-based numbering.
I determine its reading frame with the expression (position − 1) mod 3 + 1. Substituting position 7 gives (7 − 1) mod 3 + 1, which corresponds to frame +1.
Answer: Frame +1 | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | The first **ATG** begins at base **7**:
- **+1 frame:** CCG | GCT | **ATG** | …
- **+2 frame:** CG | GCT | ATG…
- **+3 frame:** C | GGC | TAT…
Therefore, the first ATG is in reading frame **+1**. | We need need parse first ATG position and frame. Sequence positions. CCG GCT ATG if frame +1: bases 1-3 CCG, 4-6 GCT, 7-9 ATG. So first ATG maybe sequence "ATG" at position? inspect CCGGCTATG yes pos7. Frame +1. Need explain numbering codons starting base1. | Step-by-step:
1. Scan the sequence from the first base for the first occurrence of **ATG**.
2. The sequence begins: C C G G C T **A T G** …, so the first **ATG** starts at base **7**.
3. Reading frames are counted from base 1:
- **+1** codons start at bases 1, 4, 7, …
- **+2** codons start at bases 2, 5, 8, …
... | The user wants me to identify the reading frame containing the first ATG in the DNA sequence CCGGCTATGCAATGAGGCTTTTGCCAAGCGTAAAGAATAGATCCTA.
Reading frames +1, +2, +3 starting from the first base.
Let me index the sequence (1-based):
Position: 1 2 3 4 5 6 7 8 9 10...
Sequence: C C G G C T A T G C A A T G A G G C T T ... | stop | {
"completion_tokens": 872,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 690,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 690
},
"prompt_tokens": 209,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
gc_mutation_effect_t3_0712 | computational | gc_mutation_effect | Consider the following two DNA oligonucleotides of identical length:
Original sequence: 5'-AGCATTAAGTGGTTTGAGT-3'
Modified sequence: 5'-AGCATTAAATGGTTTGAGT-3'
Evaluating solely on the basis of GC fraction, how does the melting temperature of the modified sequence compare to that of the original sequence? Choose from ... | To determine how the melting temperature changes between these two DNA strands, we can break the analysis down into a few clear steps:
1. Understand the relationship between base composition and melting temperature:
In DNA duplexes, guanine-cytosine pairs are joined by three hydrogen bonds, whereas adenine-thymine pai... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | **Decreased** — the modified sequence has one fewer G–C base pair (a G is replaced by A), lowering its GC fraction and therefore its melting temperature. | We need answer. Compare sequences. Original around segment AAGT vs AAAT? Original AGCATTAAGT..., modified AGCATTAAAT... One G changed to A, lowers GC fraction, Tm decreases solely GC. Need concise. | The two sequences differ by a single substitution: a **G in the original is replaced by A in the modified** sequence.
- This reduces the modified sequence’s **GC fraction** by one G/C base out of the same total length.
- Since G·C pairs contribute more to duplex stability than A·T pairs, a lower GC fraction generally ... | The user is asking about GC fraction comparison between two sequences.
Original: 5'-AGCATTAAGTGGTTTGAGT-3'
Modified: 5'-AGCATTAAATGGTTTGAGT-3'
The difference: position where original has G, modified has A. Original: AGCA TTAAGT..., Modified: AGCA TTAAAT... So one G was replaced by A.
GC fraction: original has one m... | stop | {
"completion_tokens": 258,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 158,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 158
},
"prompt_tokens": 240,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
identical_primer_template_choice_t1_0075 | computational | identical_primer_template_choice | Determine which of the two templates can be amplified by primer P alone: A, B, Both, or Neither.
Condition: For a single primer to mediate amplification on the shown strand, the template must contain the primer sequence P followed downstream (toward the 3' end) by its reverse complement.
Primer P: 5'-CCCGAGATAAGTCAG-... | First, I determine the reverse complement of primer P (5'-CCCGAGATAAGTCAG-3'). Complementing the bases gives 3'-GGGCTCTATTCAGTC-5', which reads 5'-CTGACTTATCTCGGG-3' in the standard 5' to 3' direction.
Next, I check template A for the primer sequence followed downstream by this reverse complement:
Template A contains ... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | **A**
- Primer P: `5'-CCCGAGATAAGTCAG-3'`
- Its reverse complement: `5'-CTGACTTATCTCGGG-3'`
Template **A** contains P first, followed downstream by its reverse complement. Template **B** contains these sequences in the opposite order, so P alone cannot amplify it under the stated condition. | We need inspect P and revcomp. P = CCCGAGATAAGTCAG. reverse complement? complement GGGCTCTATTCAGTC reverse CTGACTTATCTCGGG. Condition P followed downstream by revcomp in shown strand. A has P then ... and ends ... CTGACTTATCTCGGGTA, yes. B begins after CAGA CTGACTTATCTCGGG then much later P near end. That is revcomp up... | Step 1: Compute the reverse complement of primer P.
- P = 5′-CCCGAGATAAGTCAG-3′
- Reverse complement = 5′-CTGACTTATCTCGGG-3′
Step 2: Check each template for P followed downstream, toward the 3′ end, by that reverse complement.
- A: contains P early: ...CAGA**CCCGAGATAAGTCAG**TCT... and later contains **CTGACTT... | The user wants determine amplification by single primer P alone according to condition: template must contain primer sequence P followed downstream toward 3' end by its reverse complement.
Need inspect sequences. Primer P 5'-CCCGAGATAAGTCAG-3' length? CCC GAG ATA AGT CAG = 15 nt. Reverse complement of P: complement GG... | stop | {
"completion_tokens": 885,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 684,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 684
},
"prompt_tokens": 341,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
polya_signal_status_t2_0421 | computational | polya_signal_status | Take a look at the two DNA sequences provided below:
Original: 5'-CGGTCAGTGCTTCCTTTGCACTCCACCTCACACCGGCTGACTCGGAAAGACTCACGAATAAAAATGGAAAACCACGGTCCGCAAAATCCATTCTGCGGATGAAGACTCGCAAGACGAGCTC-3'
Modified: 5'-CGGTCAGTGCTTCCTTTGCACTCCACCTCACACCGGCTGACTCGGAAAGACTCACGAACAAAAATGGAAAACCACGGTCCGCAAAATCCATTCTGCGGATGAAGACTCGCAAGA... | To figure out how the canonical polyadenylation signal was affected, I need to check both sequences for the hexamer motif AATAAA, which normally serves as the cleavage and polyadenylation recognition site in eukaryotic pre-mRNA processing.
First, I scan the original sequence from 5' to 3' looking for AATAAA. Around th... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | **Disrupted**
The original sequence contains the canonical polyadenylation signal **AATAAA**, while the modified sequence changes it to **AACAAA**, disrupting the canonical motif. | We need compare. Need locate canonical AATAAA. Original around ...CACGAATAAAAAT... contains AATAAA likely positions: GAATAAAAA gives AATAAA. Modified ...CACGAACAAAAAT... substitution T->C perhaps signal becomes AACAAA, so disrupted. Check perhaps overlapping another AATAAA? Original substring AATAAAA: AATAAA yes. Modif... | 1. Locate the candidate motif region in both sequences:
- Original: `...CACGAATAAAAATGG...` → contains `AATAAA` (within `AATAAAA`).
- Modified: `...CACGAACAAAAATGG...` → the corresponding bases are `AACAAAA`.
2. Compare to the canonical polyadenylation signal `AATAAA`:
- Original matches `AATAAA`.
... | The user is asking about comparing two DNA sequences for the canonical AATAAA polyadenylation signal.
Let me find the relevant region. Both sequences have "...GACTCACGAATAAAAATGG..." in original and "...GACTCACGAACAAAAATGG..." in modified.
Original: ...CACGAATAAAAATGG...
Modified: ...CACGAACAAAAATGG...
So in the ori... | stop | {
"completion_tokens": 418,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 261,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 261
},
"prompt_tokens": 341,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
protospacer_extraction_t1_0545 | computational | protospacer_extraction | In the following DNA sequence, there is a single canonical NGG protospacer adjacent motif (PAM). Identify this site and provide the 20-nucleotide sequence located directly 5' upstream of it:
GCAGCTGAGCACACATCAATAGCCCTGCCATTAGCTGGACACTC | To determine the 20-nucleotide protospacer sequence, I will identify the PAM site and extract the upstream bases:
1. Canonical Cas9 nucleases from Streptococcus pyogenes require a 5'-NGG-3' protospacer adjacent motif (PAM) located directly downstream of the target site. I begin by scanning the provided sequence GCAGCT... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | The single canonical NGG PAM is **TGG** at positions **36–38** (the **GG** is at 37–38).
The 20-nt protospacer directly 5′ upstream of it (positions 16–35) is:
**TCAATAGCCCTGCCATTAGC** | The user wants me to find a canonical NGG PAM in the given DNA sequence and identify the 20-nt protospacer directly 5' upstream of it.
Sequence: GCAGCTGAGCACACATCAATAGCCCTGCCATTAGCTGGACACTC
Let me index the sequence (1-based):
1 G
2 C
3 A
4 G
5 C
6 T
7 G
8 A
9 G
10 C
11 A
12 C
13 A
14 C
15 A
16 T
17 C
18 A
19 A
20 T
... | 1. Scan the sequence for an **NGG** motif (any base followed by two guanines).
2. The only “GG” dinucleotide occurs at the **CTGG** region near the 3′ end, giving the PAM **TGG** (N = T).
3. The 20 nt immediately 5′ of this PAM are counted upstream ending just before the T of TGG.
**PAM:** TGG
**20-nt protospacer di... | The user wants me to find a canonical NGG PAM in the DNA sequence and provide the 20 nt directly 5' upstream of it.
Sequence: GCAGCTGAGCACACATCAATAGCCCTGCCATTAGCTGGACACTC
Let me index the sequence (1-based):
1 G
2 C
3 A
4 G
5 C
6 T
7 G
8 A
9 G
10 C
11 A
12 C
13 A
14 C
15 A
16 T
17 C
18 A
19 A
20 T
21 A
22 G
23 C
24 C... | stop | {
"completion_tokens": 910,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 782,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 782
},
"prompt_tokens": 213,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
rbs_spacing_transition_t4_0423 | computational | rbs_spacing_transition | In prokaryotic translation initiation, the Shine-Dalgarno sequence positions the ribosome appropriately upstream of the start codon, with an optimal spacer length defined as 5 to 9 nucleotides between the Shine-Dalgarno element and the ATG start codon.
Analyze the following pair of sequences:
Original: 5'-AGGAGGAGTAAA... | To evaluate how the change affects translation initiation architecture, I will determine the spacer distance between the Shine-Dalgarno motif and the start codon for both sequences. In bacteria, this spacer ensures the 16S rRNA-bound ribosome is correctly aligned with the start codon at the P site.
First, I locate the... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | - **Original:** `AGGAGG` + 6-nt spacer (`AGTAAA`) + `ATG` → **optimal**
- **Modified:** `AGGAGG` + 17-nt spacer (`GCCCTAGCGCTGGTAAC`) + `ATG` → **non-optimal**
**Classification: Reduced to non-optimal.** | We need count spacer between SD and ATG. Original AGGAGG then AGTAAA before ATG? sequence AGGAGGAGTAAATG. Identify SD likely AGGAGG, remaining AGTAAA =6 nt then ATG. optimal.
Modified AGGAGG GCCC TAG CGC TGG TAA CATG? Need ATG terminal. SD AGGAGG then sequence GCCCTAGCGCTGGTAAC =? count: GCCC(4) TAG(3)=7 CGC(3)=10 TGG... | 1. Identify the Shine-Dalgarno element as the 5′ **AGGAGG** motif in both sequences.
2. **Original:** `AGGAGG AGTAA ATG` → spacer = **AGTAA** = **5 nt**, which is within the optimal 5–9 nt range.
3. **Modified:** `AGGAGG GCCCTAGCGCTGGTAAC ATG` → spacer = **17 nt**, which is longer than 9 nt and therefore non-optima... | We need answer user. Need compute spacers. We have invoked. Now craft final with concise step-by-step. Need carefully parse sequences and definition: optimal spacer length 5-9 nt between Shine-Dalgarno element and ATG start codon. Need classify spacing change original to modified.
We need determine SD element likely A... | stop | {
"completion_tokens": 1289,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 1162,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 1162
},
"prompt_tokens": 304,
"p... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
telomere_array_change_t2_0866 | computational | telomere_array_change | Evaluate the following sequences for the tandem repeat motif TTAGGG:
Original: ACATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTGA
Modified: CGATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTCTGAGTCCGATCCG
Relative to the original sequence, has the longest uninterrupted array of thi... | 1. I first determine the size of the longest uninterrupted tandem array of the hexanucleotide repeat TTAGGG in the original sequence, ACATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTGA, which contains 5 contiguous copies.
2. I next assess the modified sequence, CGATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | **Increased.**
- **Original:** longest uninterrupted array = **5 TTAGGG repeats**
- **Modified:** longest uninterrupted array = **15 TTAGGG repeats** | We need count motif contiguous. Original after ACA? TTAGGG x5 then TTAGG? Let's inspect. "ACAT" then TTAGGG repeated? string TTAGGG TTAGGG TTAGGG TTAGGG TTAGGGTGA. Wait 5th maybe TTAGGG then TGA: ACAT + 5 repeats = ACAT +30 =34 then TGA 3 = total37. Given count maybe. Modified starts CGA then many TTAGGG then ... final... | 1. Identify the longest uninterrupted run of **TTAGGG** in each sequence.
2. **Original:** 5 consecutive copies.
3. **Modified:** 15 consecutive copies.
4. Because 15 is greater than 5, the longest uninterrupted array has **Increased**. | We need answer. Need inspect. Original motif perhaps boundary ACA +? Original listed ACATTAGGG then TTAGGG repeats etc. Need count longest uninterrupted exact TTAGGG. Original: "ACATTAGGG" contains TTAGGG starting pos4? Then four more? Let's segment AC A TTAGGG x5? Given ACATTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTGA. Remove ACA... | stop | {
"completion_tokens": 648,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 578,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 578
},
"prompt_tokens": 266,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
purine_count_0046 | dashfirst | purine_count | How many purine bases (A or G) are in this sequence? DNA: 5'-CTCTCGCTAAGA-3' | I’ll first separate the strand into individual bases: C-T-C-T-C-G-C-T-A-A-G-A. Since A and G are purines, I count 3 A bases and 2 G bases. Adding 3 and 2 gives 5.
Answer: 5 | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | There are **5 purine bases**: **3 adenine (A)** and **2 guanine (G)** bases. | We need count A G. Sequence C T C T C G C T A A G A. G positions 2, A positions 3 total 5. Need maybe explain. | Step 1: List the bases: C T C T C G C T A A G A.
Step 2: Purines are A and G; pyrimidines are C and T.
Step 3: Count A’s = 3 and G’s = 2.
Step 4: Total purines = 3 + 2 = 5.
Final answer: 5 purine bases. | The user is asking to count purine bases (A or G) in DNA sequence 5'-CTCTCGCTAAGA-3'.
Let me list bases: C T C T C G C T A A G A
Positions: 1 C, 2 T, 3 C, 4 T, 5 C, 6 G, 7 C, 8 T, 9 A, 10 A, 11 G, 12 A.
Purines are A and G. Count A: positions 9,10,12 = 3. Count G: positions 6,11 = 2. Total = 5.
Need provide concise st... | stop | {
"completion_tokens": 266,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 165,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 165
},
"prompt_tokens": 179,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
purine_count_0086 | dashfirst | purine_count | How many purine bases (A or G) are in this sequence? DNA: 5'-CAGAGCGAAGCGTGTTAAGTTTTTACCTGCACCATAAGGG-3' | To work through this problem, let us break down the given DNA strand nucleotide by nucleotide:
C-A-G-A-G-C-G-A-A-G-C-G-T-G-T-T-A-A-G-T-T-T-T-T-A-C-C-T-G-C-A-C-C-A-T-A-A-G-G-G
Recall from your biology revision that purines are adenine and guanine, represented by A and G. Now, go along the strand and tally them up care... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | There are **22 purine bases** (A or G) in the sequence — **11 A** and **11 G**. | Count A+G in sequence. Let's count carefully.
Sequence: C A G A G C G A A G C G T G T T A A G T T T T T A C C T G C A C C A T A A G G G
Index bases:
1 C
2 A p
3 G p
4 A p
5 G p
6 C
7 G p
8 A p
9 A p
10 G p
11 C
12 G p
13 T
14 G p
15 T
16 T
17 A p
18 A p
19 G p
20 T
21 T
22 T
23 T
24 T
25 A p
26 C
27 C
28 T
29 G p
30 C
... | To find the purines, count every **A** and **G** in the sequence (purines are adenine and guanine).
Sequence: `CAGAGCGAAGCGTGTTAAGTTTTTACCTGCACCATAAGGG`
Count by base:
- **A** = 11
- **G** = 11
- C = 8, T = 10 (pyrimidines, not counted)
Purines = A + G = 11 + 11 = **22**. | The user is asking me to count purine bases (A or G) in a DNA sequence. Let me carefully count.
Sequence: 5'-CAGAGCGAAGCGTGTTAAGTTTTTACCTGCACCATAAGGG-3'
Let me write it out and index each base:
C A G A G C G A A G C G T G T T A A G T T T T T A C C T G C A C C A T A A G G G
Let me count position by position:
1: C
2: ... | stop | {
"completion_tokens": 939,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 817,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 817
},
"prompt_tokens": 193,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
pyrimidine_count_0027 | dashfirst | pyrimidine_count | How many pyrimidine bases (C or T) are in this sequence? DNA: 5'-AACTGATACACCATG-3' | To determine the number of pyrimidines, examine the given sequence: A-A-C-T-G-A-T-A-C-A-C-C-A-T-G. The pyrimidines found in DNA are cytosine and thymine. A tally of these bases yields 4 cytosines and 3 thymines, which gives 4 + 3 = 7 pyrimidines altogether.
Answer: 7 | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | There are **7** pyrimidine bases: **4 C** and **3 T**. | The user is asking to count pyrimidine bases C or T in the DNA sequence 5'-AACTGATACACCATG-3'. Need provide count. Let's count carefully.
Sequence: A A C T G A T A C A C C A T G. Length 15? Let's enumerate positions:
1 A (purine)
2 A
3 C pyrimidine (1)
4 T pyr (2)
5 G
6 A
7 T pyr (3)
8 A
9 C pyr (4)
10 A
11 C pyr (5)
1... | Step 1: List the bases: A A C T G A T A C A C C A T G
Step 2: Pyrimidines are C and T. Count them: C appears 4 times; T appears 3 times.
Step 3: Total = 4 + 3 = 7.
Final result: 7 pyrimidine bases. | The user is asking to count pyrimidine bases (C or T) in DNA sequence 5'-AACTGATACACCATG-3'. Need provide concise step-by-step explanation before final result. Let's count carefully.
Sequence: A A C T G A T A C A C C A T G
Positions: 1 A,2 A,3 C,4 T,5 G,6 A,7 T,8 A,9 C,10 A,11 C,12 C,13 A,14 T,15 G.
Pyrimidines C/T: po... | stop | {
"completion_tokens": 287,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 194,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 194
},
"prompt_tokens": 182,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
pyrimidine_count_0023 | dashfirst | pyrimidine_count | How many pyrimidine bases (C or T) are in this sequence? DNA: 5'-GATTCTACTTGCAAGTCCCTCCACAACAAACCCCGTTA-3' | To find the total number of pyrimidines in the given strand, we can inspect each base along the sequence: G-A-T-T-C-T-A-C-T-T-G-C-A-A-G-T-C-C-C-T-C-C-A-C-A-A-C-A-A-A-C-C-C-C-G-T-T-A. Pyrimidines in DNA correspond to the bases cytosine and thymine, designated by the letters C and T. Walking through the sequence to tally... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | There are **23** pyrimidine bases (C or T) in the sequence.
Breakdown: **14 C’s** + **9 T’s** = **23** (out of 38 total bases). | The user is asking to count pyrimidine bases (C or T) in a DNA sequence. Let me carefully count.
Sequence: GATTCTACTTGCAAGTCCCTCCACAACAAACCCCGTTA
Let me write it out and index:
G A T T C T A C T T G C A A G T C C C T C C A C A A C A A A C C C C G T T A
Let me count character by character:
1. G - purine
2. A - purine... | Count only the pyrimidines **C** and **T** in:
`GATTCTACTTGCAAGTCCCTCCACAACAAACCCCGTTA`
- C count: 14
- T count: 9
- Total pyrimidines = 14 + 9 = **23**
**Answer: 23 pyrimidine bases** | The user wants count of pyrimidine bases C or T in given DNA sequence. Need provide concise step-by-step in final and result. Need accurately count.
Sequence: 5'-GATTCTACTTGCAAGTCCCTCCACAACAAACCCCGTTA-3'
Let's count carefully. Remove 5'/3' labels. Bases:
G A T T C T A C T T G C A A G T C C C T C C A C A A C A A A C C C... | stop | {
"completion_tokens": 819,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 726,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 726
},
"prompt_tokens": 193,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
hydrogen_bond_count_0133 | dashfirst | hydrogen_bond_count | How many hydrogen bonds form between this strand and its complement in the double helix? DNA: 5'-ATAGACAGTAA-3' | First, separate the sequence into its individual bases: A-T-A-G-A-C-A-G-T-A-A. An adenine thymine pair contributes 2 hydrogen bonds, whereas a guanine cytosine pair contributes 3. The base counts are 6 adenines, 2 thymines, 2 guanines, and 1 cytosine. Therefore, take 2 times the combined adenine and thymine count and a... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | A–T pairs form **2 hydrogen bonds**, and G–C pairs form **3 hydrogen bonds**.
Sequence `5'-ATAGACAGTAA-3'` contains:
- **8 A–T base pairs** → \(8 \times 2 = 16\)
- **3 G–C base pairs** → \(3 \times 3 = 9\)
**Total: \(16 + 9 = 25\) hydrogen bonds.** | We need need answer count base pairs A-T 2, G-C 3. Sequence length 11. Count A/T and G/C. ATAGACAGTAA: positions A,T,A,G,A,C,A,G,T,A,A. A=7? positions 1,3,5,7,10,11 =6 actually recount. Let's list: A1 T2 A3 G4 A5 C6 A7 G8 T9 A10 A11. A=6, T=2 => AT pairs 8 *2=16. G=2 C=1 =>3 GC *3=9 total25. Need perhaps complement and... | 1. **A–T base pairs form 2 hydrogen bonds.**
2. **G–C base pairs form 3 hydrogen bonds.**
3. In `5'-ATAGACAGTAA-3'`, there are:
- 8 A/T bases → \(8 \times 2 = 16\) hydrogen bonds
- 3 G/C bases → \(3 \times 3 = 9\) hydrogen bonds
\[
16+9=\boxed{25}
\]
**The strand forms 25 hydrogen bonds with its complement.** | We need need count A-T 2, G-C 3. Sequence 11 bases. Count A/T vs G/C. A T A G A C A G T A A: A positions 1,3,5,7,10,11 =6; T 2; G2; C1. AT pairs 8*2=16; GC 3*3=9 total25. Explain complement maybe TATCTGTCATT. | stop | {
"completion_tokens": 222,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 94,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 94
},
"prompt_tokens": 180,
"prompt... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
k0062 | knowledge | cluster_6 | A rat conditional allele contains loxP sites on either side of exons 2 and 3, and both sites point toward the telomere. What is the expected genomic allele after Cre recombination? | The two loxP sites are in the same orientation, so Cre recombination excises the DNA between them as a circular fragment. The chromosome retains one loxP site and loses exons 2 and 3, generating a deletion allele.
Answer: A genomic allele lacking exons 2 and 3, with one residual loxP site at the recombination junction... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | Because the two loxP sites are in the **same orientation**, Cre-mediated recombination will **delete the intervening genomic segment containing exons 2 and 3**. The resulting allele retains **one residual loxP site** at the deletion junction, while the excised exon 2–3 fragment is typically lost. | We need need infer orientation both same direction yields deletion of intervening exons, one loxP remains. Need perhaps caveat cis recombination. Wording both point toward telomere = same orientation. Expected floxed segment deleted circular extrachromosomal, lox sites recombine. In allele sequence exons2/3 absent. Nee... | 1. Both loxP sites have the **same orientation** (toward the telomere).
2. Cre recombinase recognizes and recombines the two sites.
3. Same-oriented loxP sites cause **deletion of the intervening DNA**, leaving behind a single loxP site.
**Expected allele:** a deletion allele lacking **exons 2 and 3**, with one re... | We need answer. Same orientation flanking region => deletion of intervening sequence, leaves one loxP. Need perhaps clarify telomere orientation irrelevant, same direction. Exons 2 and 3 removed. Conditional null after Cre. Step-by-step concise. | stop | {
"completion_tokens": 166,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 53,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 53
},
"prompt_tokens": 191,
"prompt... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
k0417 | knowledge | cluster_13 | A mouse Vegfa enhancer contains a HIF-1 response element 5′-ACGTG-3′, matching the HIF core consensus RCGTG. A mutation changes it to 5′-ACTTG-3′. What outcome is expected under hypoxia? | The normal sequence ACGTG matches the HIF-1 core consensus RCGTG.
Changing the central G to T produces ACTTG, which no longer matches the core HIF-1 binding motif.
Therefore, HIF-1 binding and enhancer activation would be strongly reduced or abolished under hypoxia, causing decreased hypoxia-induced Vegfa transcripti... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | The mutation disrupts the HIF core motif (RCGTG → RCTTG), likely markedly reducing or abolishing HIF-1 binding. Consequently, the enhancer should show substantially diminished—or lost—hypoxia-induced activation, resulting in reduced hypoxic induction of **Vegfa** (assuming no compensatory HIF sites are present). | We need answer likely reduced/abolished HIF binding and induction. Need clarify core consensus mismatch: ACGTG to ACTTG changes G to T at third position, destroys core. Under hypoxia reduced enhancer activity/Vegfa transcription. Maybe no induction. Mention other elements possible. | Step-by-step:
1. HIF-1 is stabilized under hypoxia and binds HREs containing the core consensus **5′-RCGTG-3′**, where R = A/G.
2. The wild-type sequence **ACGTG** matches this consensus, so hypoxia would normally increase HIF-1 binding and enhancer-driven **Vegfa** transcription.
3. The mutant **ACTTG** changes ... | We need answer biology. Need provide concise step-by-step explanation and final. Let's reason: HIF-1 binds hypoxia response elements core 5'-RCGTG-3' (R=A/G). Given enhancer has ACGTG matches (A at R). Mutation ACTTG changes third? Compare A C G T G vs A C T T G: position3 G->T within core CGTG? HIF core is R C G T G; ... | stop | {
"completion_tokens": 411,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 210,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 210
},
"prompt_tokens": 208,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
k0436 | knowledge | cluster_10 | The Salmonella enterica salB fragment 5′-GGGAGGAGGCTCGTAGTGAAATGCCC-3′ contains candidate GTG and ATG starts. Which is favored by Shine–Dalgarno logic? | The likely Shine–Dalgarno sequence is AGGAGG at positions 4–9.
For the GTG start at positions 16–18, the spacer is 6 nucleotides long, which is near the preferred bacterial spacing.
For the ATG start at positions 21–23, the spacer is 11 nucleotides long, which is less favorable.
Thus, despite ATG being the more comm... | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | The **GTG start** is favored.
The sequence contains a strong Shine–Dalgarno–like motif:
**5′-GGG AGGAGG CTCGTA GTG AAA TGC CC-3′**
- **SD motif:** AGGAGG, complementary to the 3′ end of 16S rRNA
- **Spacing to GTG:** six nucleotides (CTCGTA), within the optimal ~5–10 nt range
- **ATG** lies farther downstream an... | We need analyze sequence. Need identify upstream SD motif relative starts. Sequence 5' GGG AGG AGG CTC GTA GTG AAA TGC CC. Candidate GTG at positions? index: GGG 1-3, AGG 4-6, AGG7-9, CTC10-12, GTA? Sequence CTCGTAGTG... Let's index exact. GG G A G G A G G C T C G T A G T G A A A T G C C C. indices 1 G 2 G 3 G 4 A 5 G ... | 1. The strong Shine–Dalgarno-like motif is **AGGAGG** near the 5′ end.
2. The downstream **GTG** start is about six nucleotides from this motif, within the typical ribosome-binding spacer range.
3. The candidate **ATG** is much farther downstream, giving an unusually long spacer and therefore weaker Shine–Dalgarno posi... | We need analyze spacing SD sequence AGGAGG likely, downstream GTG? Sequence GGG AGGAGG CTC GTA GTG AAA TGC CC. Candidate GTG at positions maybe 15, ATG 21? SD core AGGAGG ends pos10. GTG starts? index: GGG 1-3, AGGAGG 4-9? string length count. Let's index accurately: G1 G2 G3 A4 G5 G6 A7 G8 G9 C10 T11 C12 G13 T14 A15 G... | stop | {
"completion_tokens": 388,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 248,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 248
},
"prompt_tokens": 197,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
k0865 | knowledge | cluster_11 | An Escherichia coli plasmid carrying bla is cut once with BamHI, whose cleavage pattern is 5′-G^GATCC-3′, and then self-ligated without end processing. What sequence spans the ligation junction? | BamHI cuts to produce complementary 5'-GATC overhangs. Because the plasmid is self-ligated without end processing, these overhangs anneal and ligase restores the original BamHI recognition site.
Answer: 5'-GGATCC-3' paired with 3'-CCTAGG-5' | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | The BamHI site is regenerated:
**5′-GGATCC-3′**
**3′-CCTAGG-5′**
BamHI leaves complementary 5′-GATC overhangs, so self-ligation without end processing restores the original recognition sequence. | We need answer trick ambiguity? BamHI sticky ends self ligate regenerates site GGATCC. But sequence spans junction perhaps GGATCC. Need explain orientation. Cleavage after G: 5' GATC overhang. Religation restores GGATCC. Could issue plasmid carrying bla irrelevant. "without end processing". Junction is original BamHI s... | 1. BamHI cuts **once** at the sequence **5′-GGATCC-3′**, between the two guanines:
\[
5'{-}G\ \vert\ GATCC{-}3'
\]
2. Self-ligation joins the compatible **GATC** cohesive ends directly, without fill-in or trimming.
3. Therefore, the original BamHI recognition site is regenerated.
**Ligation-junction sequence:... | We need explain compatible cohesive ends regenerate BamHI site likely GGATCC, but ambiguity strand context? Cut one site, self ligate restores exact sequence. "without end processing." Junction sequence GGATCC. Need perhaps 5' to 3'. Explain stagger cuts G overhang? BamHI cuts G^GATCC on both strands: 5'-G | GATCC, bot... | stop | {
"completion_tokens": 235,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 108,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 108
},
"prompt_tokens": 204,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
k0937 | knowledge | cluster_0 | A candidate human NANOG enhancer contains 5′-ATGCAAAT-3′ in an OCT4-positive embryonic stem cell. What cis-regulatory motif is present? | The sequence 5′-ATGCAAAT-3′ is the canonical octamer DNA motif recognized by the OCT4/POU5F1 transcription factor.
Answer: OCT4-binding octamer motif (5′-ATGCAAAT-3′) | Answer the user's question. Your visible final answer must include a concise, self-contained
step-by-step explanation before the final result. Do not return only the final result. Keep the explanation focused,
and do not mention hidden reasoning or these instructions. | moonshotai/Kimi-K3:fireworks-ai | low | The sequence **5′-ATGCAAAT-3′** is the **octamer (OCT) motif**, a binding site for **POU-family transcription factor OCT4**. | We need answer motif octamer, OCT4/SOX2? ATGCAAAT is octamer motif recognized by POU family Oct4. Need perhaps OCT4-binding motif. Concise. | The sequence **5′-ATGCAAAT-3′** matches the consensus **octamer motif** recognized by POU-family transcription factors.
Step-by-step:
1. Compare the enhancer sequence to known TF-binding consensus motifs.
2. **ATGCAAAT** is the canonical **Oct4/POU5F1 octamer element**.
3. In OCT4-positive embryonic stem cells, ... | The user is asking about a DNA sequence 5'-ATGCAAAT-3' in context of human NANOG enhancer, OCT4-positive ESC. Need identify cis-regulatory motif. This sequence is the octamer motif / POU domain binding site, consensus ATGCAAAT, bound by OCT4 (POU5F1) and SOX2 often nearby. NANOG enhancer contains Oct4/Sox2 binding site... | stop | {
"completion_tokens": 354,
"completion_tokens_details": {
"accepted_prediction_tokens": null,
"audio_tokens": null,
"reasoning_tokens": 207,
"rejected_prediction_tokens": null,
"text_tokens": null
},
"output_tokens_details": {
"reasoning_tokens": 207
},
"prompt_tokens": 186,
"prom... | HuggingFaceBio/basic-dna-sft-data | all_decontaminated | be1e789606e41af5c2b92d450223b994386b9ed8 |
| subset | description | num_samples |
|---|---|---|
low_visible_cot_20 |
Kimi K3 low-effort outputs explicitly prompted to include concise reasoning in the visible answer | 20 |
Basic DNA Kimi K3 visible-reasoning pilot
These outputs test whether moonshotai/Kimi-K3:fireworks-ai with reasoning_effort="low" includes a concise, self-contained explanation in
the visible answer when explicitly requested. The dataset retains both the visible content and the separate
reasoning_content returned by the API, along with the corresponding response from the earlier answer-only run.
The 20 prompts are selected deterministically with seed 42: 10 from the computational track, 5 from dashfirst, and
5 from knowledge. The source is HuggingFaceBio/basic-dna-sft-data, config all_decontaminated, revision be1e789606e41af5c2b92d450223b994386b9ed8.
Generation settings
- Model:
moonshotai/Kimi-K3:fireworks-aithrough the Hugging Face inference router and Fireworks - Reasoning effort:
low - Maximum completion tokens: 8,192
- Visible-answer instruction: recorded verbatim in every row's
instructionfield
Reproducing
The exact published responses are retained under raw/. Rebuild and optionally republish the dataset with:
hf download edbeeching/basic-dna-kimi-k3-outputs-261006 \
--repo-type dataset \
--include 'raw/*' 'scripts/create_dataset.py' \
--local-dir basic-dna-kimi-k3-outputs-261006
python basic-dna-kimi-k3-outputs-261006/scripts/create_dataset.py \
--input-jsonl basic-dna-kimi-k3-outputs-261006/raw/kimi_k3_low_visible_cot_20.jsonl \
--output-dir basic-dna-kimi-k3-outputs-261006/rebuilt
The original API generation implementation is published as scripts/generate_outputs.py. It uses the pinned source
revision above and requires HF_TOKEN to issue new requests.
- Downloads last month
- 150