Computational protocol: Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus

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Protocol publication

[…] The use of both TBLASTN with 18 query transposases and MEGABLAST allowed us to identify more than 3685 copies representing 36 different mariner lineages. TBLASTN provided several hits that were identified as Tc1-like sequences, which indicates that the search was likely to be exhaustive. However, non-autonomous lineages could have been missed because we did not recover too-short sequences (<400 bp) or sequences with no conserved transposase domain, generated by internal deletions. Copies interrupted by insertions of less than 1000 nt could be reassociated. However, if an insertion is longer than 1000 nt, one copy could appear as two independent truncated copies. However, this imprecision is not expected to strongly bias the results. Hence, the panel of retrieved copies can be considered as representative of the mariner panorama in the Drosophila sequenced genomes. […]

Pipeline specifications

Software tools TBLASTN, BLASTN
Application Amino acid sequence alignment
Organisms Drosophila melanogaster