Computational protocol: Slip-Sliding Away: Serial Changes and Homoplasy in Repeat Number in the Drosophila yakuba Homolog of Human Cancer Susceptibility Gene BRCA2

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Protocol publication

[…] DNA sequences were aligned computationally using BioEdit 7.0.9 , and then modified by manual alignment. DNAsp was used to estimate nucleotide diversity (pi) and Tajima's D , for the dmbrca2 region. We obtained the values of Tajima's D for similar loci in D. yakuba and D. santomea from Llopart et. al. for comparison.We examined the sequenced regions for each strain and compared them to the full assembled sequence of this region from the published D. yakuba genome . In the published genome region, we categorized the five distinct BRC repeats using diagnostic amino acids and size differences, numbering them numerically 1 through 5 from the 5′ end . We translated the DNA sequence of the exons of our strains' sequences and manually compared each individual repeat to the numbered genome repeats using the diagnostic amino acids and size differences.Phylogenetic analysis was performed with PAUP* 4.0b10 . BRCA2 repeat motifs for D. melanogaster (Dme), D. sechellia (Dse), D. simulans (Dsi), D. erecta (Der), and D. yakuba (Dya) were obtained from the FlyBase reference genomes, and combined with D. santomea (Dsa) and additional D. yakuba sequences collected for this work. D. yakuba was used as a standard for numbering repeat motifs: 1–5 from the amino-end to carboxyl-end of peptide. D. persimilis repeat 2 (Dpe2) was used as an outgroup. Sequence alignments were done in Seaview version 4.0 with additional adjustments by eye. The sequence motifs were delineated by the 35 amino acid long Pfam hidden Markov model (HMM) for BRCA2 repeats . Due to the short sequence length and modest levels of sequence variation, neighbor-joining with uncorrected p-distances was chosen for tree estimation. […]

Pipeline specifications

Software tools BioEdit, DnaSP, PAUP*, SeaView
Databases FlyBase Pfam
Application Phylogenetics
Organisms Drosophila melanogaster, Drosophila yakuba, Homo sapiens, Drosophila santomea
Diseases Breast Neoplasms, Neoplasms