A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species

Hawkins, John A.; Kaczmarek, Maria E.; Müller, Marcel A.; Drosten, Christian; Press, William H.; Sawyer, Sara L.

Next, we added orthologs from the transcriptomes. First, genomic transcripts were translated to amino acid sequence, and blastx-tblastn reciprocal BLAST hits were found between all genomic high-quality orthologous genes and all transcriptome assemblies, again using an e-value cutoff of 10 −5 . We then created HMMER models of each of the genomic orthologous gene sets and searched within the reciprocal BLAST hit contigs for the best HMMER hit for each gene, filtering for those hits with e value below 10 −10 , extracting only the portion of each contig specified in the HMMER hit. We then filtered all transcripts which differed in length from the median genomic sequence length by more than 25%.