Inference chain: Methodological rationale for HGT and viral capsid detection

InferenceChain·arcadia

This chain explains the reasoning and analytical approaches underpinning the detection and interpretation of viral capsid horizontal gene transfer (HGT) events, including methodological choices such as the use of sequence similarity search (HMMER), pipeline workflows (PreHGT), and database curation for efficient candidate screening. It also covers reliance on prior literature to benchmark detection frameworks and exclude false positives.

Confidence

80%

◑partialactivecomplexity: mid

Reasoning Steps (3)

Use of HMMER for sensitive sequence similarity screeningStep 1

Pipeline, benchmarking, and database reductionStep 2

Reference to known HGT and comparative toolsStep 3

Source

Synthesis for current paper

Connections (4)

Alien index predicts HGT eventsAssociation

Putative endogenized viral capsid proteins in ticks from HGTAssociation

Capsid HMM sequence enables detection of putative viral capsidsAssociation

HGT detection identifies capsid genes in ticksAssociation