Skip to main content
Glama

In-silico PCR

in_silico_pcr
Read-onlyIdempotent

Predict PCR products for a template and a pair of primers (IUPAC-aware, allows mismatches, handles circular templates). Primers may carry a non-templated 5' tail — a restriction site, a Gibson arm, a Kozak, a tag: a primer primes on its 3' end, and the tail is carried into the product rather than required to match. start/end are the TEMPLATE-derived span, length is the whole product including tails, and features marks which product bases came from the oligos (present only when there is a tail). Each end reports annealedLength and tailLength.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
circularNoTreat the template as circular (plasmid).
templateYesNucleotide sequence (raw or FASTA; IUPAC accepted).
forwardPrimerNoPrimer 1, 5'→3'.
maxMismatchesNoMismatches tolerated per primer (0–10).
reversePrimerNoPrimer 2, 5'→3' (order does not matter). Optional: one primer alone is accepted and reports the products it makes on its own — none, unless the template carries inverted sites it can prime from both ends.
maxProductLengthNoIgnore predicted products longer than this (bp). A SEARCH WINDOW, not a claim about what amplifies: whole-plasmid inverse PCR — the reaction a q5-style site_directed_mutagenesis design is run as — makes one product the size of the plasmid, so raise this for a construct over 50 kb. `suppressedByLength` in the response counts what the window discarded.

TDQS

A4.6/5.0
Behavior5/5

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

Annotations already declare readOnlyHint=true and idempotentHint=true, but the description goes far beyond that. It explains the non-templated 5' tail behavior, clarifies that primers prime on the 3' end, defines start/end as template-derived span and length as including tails, and mentions the 'features' field and per-end annealedLength/tailLength in the output. This rich behavioral context, including edge cases like circular templates and search-window semantics for maxProductLength, adds substantial transparency.

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

Conciseness5/5

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

The description is dense but every sentence earns its place. The core purpose leads, followed by the tail mechanism, then parameter semantics. There is no fluff or repetition, and technical details like the start/end vs length distinction are packed efficiently. It is appropriately long for the complexity but remains tightly structured.

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

Completeness5/5

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

Given 6 parameters, no output schema, and a complex tool, the description covers everything an agent needs to call it correctly: primer orientation, tail handling, circular behavior, mismatch tolerance, and even the semantics of maxProductLength plus the response fields (features, annealedLength, tailLength, suppressedByLength). It is fully self-contained despite the absence of an output schema.

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

Parameters5/5

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

The schema already provides descriptions for all 6 parameters (100% coverage), but the description adds crucial nuance: it clarifies that reversePrimer is optional and order-independent, explains the tail interpretation for forwardPrimer, and reinterprets maxProductLength as a 'SEARCH WINDOW' that discards products via suppressedByLength. This goes well beyond the schema to resolve ambiguity and correct potential misinterpretations.

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 immediately states the specific verb and resource: 'Predict PCR products for a template and a pair of primers'. It further distinguishes itself by listing key capabilities (IUPAC-aware, allows mismatches, handles circular templates) that separate it from primer design tools like primer_design. This makes its purpose clear and non-confusable with siblings.

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?

Usage is implied rather than explicit. The description says what it does but never directly states when to use it over alternatives or when not to use it. The only hint is the mention of 'whole-plasmid inverse PCR' in the maxProductLength parameter, which implicitly ties it to cloning workflows but does not contrast with other sibling tools. There is no explicit when/when-not guidance.

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

Try in Browser

Glama MCP Gateway

Add one secure layer between your agents and this server.

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.

Resources