Computational protocol: DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs

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Protocol publication

[…] All Osmar sequences were previously described and their accession numbers are available in Feschotte et al. (). Osmars were mined from two databases, one containing ∼360 Mb of BAC/PAC sequences from O.sativa ssp. japonica cv. Nipponbare (downloadable at ) and the second containing ∼430 Mb of contigs generated by whole-genome sequencing of O. sativa ssp. indica cv. 9311 (downloadable at ). Stowaway families were previously identified in the genomic sequence of O. sativa ssp. japonica cv. Nipponbare and their assignment to corresponding Osmar clades has been described (). Consensus sequences for each Stowaway family are available through Repbase () or upon request. Predictions for helix-turn-helix motifs were carried out with the method of Dodd and Egan () through the Network Protein Sequence Analysis website (). To generate the tree shown in , full-length Osmar transposase sequences were aligned with ClustalW using default parameters in MacVector 7.0 and the alignment was trimmed to preserve only the regions that align with the first 206 amino acids of Osmar5 (see ). The resulting phylogenetic tree was generated with PAUP* Version 4.0b8 () using the neighbor-joining method with default parameters and rooted at the midpoint. All other sequence manipulations were performed with MacVector 7.0 or as described in Feschotte et al. (). […]

Pipeline specifications

Software tools Clustal W, MacVector, PAUP*
Databases Repbase
Application Phylogenetics
Organisms Oryza sativa