Computational protocol: Evolutionary Conservation of pou5f3 Genomic Organization and Its Dynamic Distribution during Embryogenesis and in Adult Gonads in Japanese Flounder Paralichthys olivaceus

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Protocol publication

[…] The exon and intron boundaries were determined by alignment of the obtained cDNA sequence with the generated genome sequence. NCBI′s online ORF Finder and DNASTAR were employed to predict ORF for translated peptide product. The POU domains were identified using the simple modular architecture research tool (SMART) and InterProScan search software. The multiple alignments of Pou5f3 were generated with ClustalW and the phylogenetic tree was constructed using the MEGA 5.2 program by the neighbor-joining method with 1000 bootstrap replicates. Bioinformatic analysis and potential transcription factor binding sites within the 5′ regulatory region of Popou5f3 was performed with online program MatInspector. The conserved promoter sequences between fish and mammals were analyzed by the MEME software and the Dialign software from the Genomarix suite. The websites of the software mentioned above were listed in . […]

Pipeline specifications

Software tools Open Reading Frame Finder, InterProScan, Clustal W, MatInspector, DIALIGN
Databases SMART
Application Phylogenetics
Organisms Paralichthys olivaceus, Homo sapiens