Computational protocol: Comparative Genomics Reveals Key Gain-of-Function Events in Foxp3 during Regulatory T Cell Evolution

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Protocol publication

[…] All sequences were retrieved from the NCBI, UCSC, and Ensembl databases before January 2012. For BLAST analyses, mouse Foxp proteins were used for NCBI or Ensembl BLASTP and NCBI TBLASTN (databases: nr/nt and est_others). Specifically for Foxp3 proteins the following accession numbers were used: mouse (NP_473380), lizard (ENSACAP00000013243; partial sequence), opossum (XP_001372400), platypus (XP_001507281/ENSOANP00000021424), frogs (BAG12188.1 and NP_001121199.1), zebrafish (ACQ44666), salmon (NP_001185776), rainbow trout (CAT65091), stickleback (ENSGACP00000016881), and tetraodon (ENSTNIP00000007498). […]

Pipeline specifications

Software tools BLASTP, TBLASTN
Application Amino acid sequence alignment
Organisms Homo sapiens