SECISaln

SECISaln predicts and aligns eukaryotic SECIS (Selenocysteine Insertion Sequence) RNA stem-loop elements to identify conserved nucleotide positions and analyze SECIS secondary structure in selenoprotein mRNAs.

Key Features:

• SECIS prediction: Predicts the presence of SECIS elements within input sequences, including recognition of SECIS in the 3' untranslated region (UTR) of selenoprotein mRNAs associated with in-frame UGA codons encoding selenocysteine.
• Element deconstruction: Deconstructs SECIS elements into constituent structural components for detailed analysis.
• Structure-based alignment: Performs structure-based sequence alignments that leverage the conserved SECIS secondary structure to align sequences with limited primary sequence conservation.
• Database alignment: Aligns SECIS components against a comprehensive database of eukaryotic SECIS elements.
• Conserved site identification: Identifies novel conserved nucleotide positions and structural features across aligned SECIS elements.
• Cross-species comparison: Enables comparative analysis of SECIS secondary structure across eukaryotic species.

Scientific Applications:

• SECIS detection: Detection and confirmation of SECIS elements in eukaryotic selenoprotein mRNAs.
• Conserved motif discovery: Discovery of conserved nucleotide positions and structural motifs within SECIS elements.
• Selenocysteine incorporation studies: Investigation of mechanisms of selenocysteine incorporation at in-frame UGA codons.
• RNA structure and evolution: Comparative studies of RNA secondary structure and the evolution of SECIS elements across eukaryotes.

Methodology:

Predicts SECIS presence, deconstructs elements into constituent parts, and performs structure-based sequence alignments of those components against a database of eukaryotic SECIS elements.