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Primer Tm calculator

melting_temperature
Read-onlyIdempotent

Primer/oligo melting temperature: nearest-neighbour (SantaLucia 1998) at the supplied reaction conditions, recommended from 14 nt up, with the Wallace rule for shorter oligos, a fixed-100 mM-Na+ Schildkraut-Lifson reference estimate, and molecular weights.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
mgMMNoDivalent cation [Mg2+] (mM).
naMMNoMonovalent cation [Na+]/[K+] (mM).
dntpMMNoTotal [dNTP] (mM), chelates Mg2+.
oligoNMNoTotal strand concentration (nM).
sequenceYesNucleotide sequence (raw or FASTA; IUPAC accepted).
targetTmNoOptional target Tm (°C). When given, the response includes a pass/fail gate.
tmToleranceNoAllowed +/- window (°C) around targetTm for the gate.

TDQS

A3.6/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already indicate read-only and idempotent behavior. The description adds methodological context (nearest-neighbour, Wallace rule, Schildkraut-Lifson) but does not detail return format, the pass/fail gate for targetTm, or potential limitations like sequence length restrictions beyond the 14 nt recommendation.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, information-dense sentence that front-loads the core purpose. It includes relevant details without excessive filler, though the listing of multiple thermodynamic methods makes it slightly heavier than necessary.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a calculation tool with 7 parameters and no output schema, the description explains what it computes and the methodology, but it does not explain the optional targetTm pass/fail gate or what the response contains beyond molecular weights. It also lacks explicit comparison to sibling oligo analysis tools, which would help in a rich tool ecosystem.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100% with parameter descriptions, so the baseline is 3. The description's mention of 'supplied reaction conditions' and 'molecular weights' adds context to parameters like mgMM and oligoNM but does not directly map to parameter syntax or required input formats.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with 'Primer/oligo melting temperature' clearly stating the tool's function. It further specifies the calculation method (nearest-neighbour SantaLucia 1998) and includes molecular weights, distinguishing it from sibling tools like primer_design or cross_dimer.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage for Tm calculation and offers some guidance by noting the 14 nt length recommendation and the Wallace rule for shorter oligos. However, it does not explicitly state when to use this tool over alternatives or provide exclusions, such as when to choose primer_design or oligo_analysis.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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TDQS

A3.6/5.0
Disambiguation4/5

Most tools have highly specific purposes (e.g., crispr_grna_design vs base_editing_design vs prime_editing_design). However, there is some overlap in sequence analysis tools (characterize_sequence, sequence_report) and plasmid annotation tools (plasmid_annotate vs plasmid_deep_annotate) which could cause confusion.

Naming Consistency3/5

The naming pattern is largely consistent with snake_case verb_noun or noun_descriptor (e.g., primer_design, plasmid_annotate, fastq_trim). However, there are exceptions like 'batch', 'workflow', 'gc_content', and 'cloning_diagnose' which don't follow the verb_noun pattern consistently. Also, some names are phrases like 'golden_gate_from_parts'.

Tool Count2/5

With 101 tools, this server is extremely large and likely overwhelming for agents. Even for a comprehensive bioinformatics toolkit, this exceeds a manageable scope, risking agent confusion and inefficient tool selection. A more modular approach would be advisable.

Completeness4/5

The tool surface covers a wide range of bioinformatics workflows including sequence analysis, primer design, cloning, CRISPR, NGS, expression analysis, and data export. There are minor gaps such as lack of a dedicated protein structure prediction tool and limited off-target genome coverage, but overall the set is impressively complete for its domain.

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