Computational protocol: Ribosomal Readthrough at a Short UGA Stop Codon Context Triggers Dual Localization of Metabolic Enzymes in Fungi and Animals

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Protocol publication

[…] For the identification of C-terminal protein extensions containing a peroxisomal targeting signal the TransTerm database was used to retrieve 3′ flanking sequences from several organisms. The sequences were processed using regular expressions to retain only sequences between the regular stop codon to the next in-frame stop codon. Sequences were translated using Virtual Ribosome . C-terminal tripeptides of the translated sequences were scanned for putative PTS1 motifs using the following regular expression:(∧\*[∧*]*?([ASTPCE]RL|[SATPCVNG]KL|S[SNH]L|ARI|S[KR]M|[AG]NL|SN[IM]|[SA][KRQ]Y|HHL|[QS][KRQ]F)\*). PTS2 motifs were predicted with TargetSignalPredictor (http://www.peroxisomedb.org). Data analysis was performed with NCBI (National Center for Biotechnology Information) Basic local alignment search tool (Blast) , other NCBI resources and GenRE - MIPS Ustilago maydis DataBase. […]

Pipeline specifications

Software tools Virtual Ribosome, BLASTN
Databases PeroxisomeDB Transterm
Application Genome annotation
Organisms Homo sapiens
Chemicals NAD, Lactic Acid