Computational protocol: Computational identification of functional introns: high positional conservation of introns that harbor RNA genes

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Protocol publication

[…] The phylogenetic tree for the 28 species was formed by combining taxonomic data from The Tree of Life Web Project (http://tolweb.org/), NCBI (,) and FlyBase (). Divergence times were estimated based on Time Tree (). iTOL () was used for tree display and modification (Supplementary Figure S1). When there were no data on the divergence time between two species, we used sequences with orthologs in close species with known divergence time to reconstruct the phylogeny using UPGMA (). Then, we estimated the missing divergence times by linear regression. As future analysis steps require a bifurcating tree, multifurcations were resolved by a series of bifurcations, separated by short (100 000 years) internal branches. [...] We used MUSCLE () to align the protein products of the transcripts within each set of orthologs, then applied the Matlab function seqinsertgaps to get the multiple alignment at the mRNA level. […]

Pipeline specifications

Software tools iTOL, MUSCLE
Databases FlyBase
Applications Phylogenetics, Nucleotide sequence alignment