Help & glossary

Glossary

IRES

Internal ribosome entry site — an RNA element that recruits the ribosome independently of the 5′ cap.

IRESG (IRES group)

A family of IRES sequences clustered by sequence/structure similarity, with a seed alignment, a consensus secondary structure and a calibrated covariance model.

Evidence class

How a family is supported: anchored to a public Rfam model, or de novo (graph clustering, residual rescue, or type-driven).

Production route

The pipeline branch that produced the final family (RouteA–RouteF).

Orphan sequence

A candidate IRES not assigned to any family. Unassigned does not mean non-IRES.

Core / flank

The core region is the aligned, modelled part of an IRES; flanks are the surrounding UTR context exported alongside it.

Activity

Experimental IRES activity from a FACS-based reporter assay over a tested sequence subset. A family's median activity is computed only over members with measurements (activity_n_measured); families with no measured members show "no data". The number of measured members says nothing about family size — most families have no tested members yet.

Methods in brief

Candidate IRES regions are extracted from viral genome 5′UTR and intergenic regions, embedded and clustered, then refined into families with covariance models (Infernal). Each family ships with its calibrated CM, seed alignment and consensus structure, so results are searchable and reproducible.

FAQ

Why does a family have no type label?

Most families are de novo discoveries without a curated type assignment; they are named De novo family N and described by their evidence class and production route.

Can I search my own sequence?

A cmsearch-based similarity search is planned. Meanwhile you can download the CM package and run cmsearch locally.