SECISearch3 Seblastian

SECISearch3 Seblastian identifies selenoproteins by detecting eukaryotic SECIS stem-loop elements in 3' untranslated regions (UTRs) that mediate UGA-to-selenocysteine (Sec) recoding and by predicting upstream selenoprotein coding sequences for annotation and evolutionary analysis.

Key Features:

• SECISearch3: Predicts eukaryotic SECIS stem-loop elements in 3' UTRs that enable UGA-to-Sec translational recoding.
• SeBLASTian: Predicts selenoprotein sequences encoded upstream of identified SECIS elements and identifies candidate Sec residues.
• Ranked prediction and homologue annotation: Produces a ranked list of newly predicted selenoproteins alongside annotated cysteine-containing homologues.
• Genome-scale eukaryotic analysis: Applies SECIS detection and upstream sequence prediction across diverse eukaryotic genomes for comprehensive selenoprotein identification.

Scientific Applications:

• Selenoprotein discovery and annotation: Identification and annotation of known and novel selenoproteins by combining SECIS element detection with upstream coding-sequence prediction.
• Evolutionary analysis: Comparative study of Sec/Cys substitutions and selenoprotein distribution across lineages, exemplified by analyses of the AhpC family.
• Molecular genetics and proteomics: Investigation of translational recoding mechanisms involving SECIS elements and UGA stop codon reassignment to selenocysteine.

Methodology:

SECISearch3 predicts eukaryotic SECIS stem-loop elements in 3' UTRs; SeBLASTian predicts selenoprotein coding sequences upstream of identified SECIS elements and generates ranked predictions with annotated cysteine-containing homologues.