Computational protocol: The genomic environment around the Aromatase gene: evolutionary insights

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Protocol publication

[…] The gene content around the CYP19 human gene in chromosome 15 comprises eight open reading frames (ORFs) within a DNA sequence of 1.0 Mb (figure ). These are annotated as follows: AP4-E1 [GenBank: NP_031373], FLJ41287 (SSC-2SC) [GenBank: NP_997264], Collomin [GenBank: NP_861454], DMXL2 [GenBank: NP_056078], SCGIII [GenBank: NP_037375], MGC35274 [GenBank: NP_699205], TMOD2 [GenBank: NP_055363], and TMOD3 [GenBank: NP_055362] (figure ). In order to find invertebrate orthologues and vertebrate paralogues, protein sequence from each gene was extracted and used for BLAST search (TBLASTN) against GenBank and Ensembl. Accession numbers for each gene are given in table .Putative protein sequences for each gene family were aligned using the CLUSTAL X program (version 1.8). The produced alignments were further edited by eye to maximise the homologous regions (conserved domains) (given upon request). The phylogenetic reconstruction was based on conserved domains. If no domains were identified, reconstruction's were performed using the full-length alignment (without taking into account gaps or ambiguous sites). The phylogenetic trees were constructed using neighbor-joining from the CLUSTAL X program, on an amino acid distance matrix calculated with the Dayoff PAM option. Confidence on each node was assessed by 1000 bootstrap replicates. Trees were visualised with the Treeview program (version 1.6.6).Mapping data was retrieved from H. sapiens [], T. nigroviridis [], X. tropicalis [] and C. intestinalis []. […]

Pipeline specifications

Software tools TBLASTN, Clustal W, TreeViewX
Applications Phylogenetics, Amino acid sequence alignment
Organisms Homo sapiens, Tetraodon nigroviridis, Xenopus tropicalis, Branchiostoma floridae, Branchiostoma lanceolatum
Chemicals Androgens, Estrogens