Computational protocol: IP6K gene identification in plant genomes by tag searching

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Protocol publication

[…] For each identified tag, we extracted a sequence of about 1200 nucleotides surrounding the consensus sequence and examined it as a candidate IP6K gene. Nucleotidic sequences were translated in aminoacid sequences by using the Transeq [] software. Then, we examined the identified amino acid sequences looking for other IP6Ks conserved domains. In order to detect possible homologies, we performed sequence alignments using ClustalW [] and BLAST []. Finally, using the TBLASTX and TBALSTN algorithms, we screened expressed sequence tag (EST) databases for proteins containing the sequences identified by our tag search.In the following, we first provide a brief description of DLSME and of the setting we exploited for our purposes, and then describe the main results we have obtained by our analysis. […]

Pipeline specifications

Software tools Clustal W, TBLASTX
Application Nucleotide sequence alignment
Organisms Homo sapiens, Oryza sativa
Chemicals Lead, Nucleotides, Phosphates, Polyphosphates, Potassium