Figure 1.

Workflow for the parallel 2-pass BLAST procedure used for generating InParanoid 8. BLAST runs are launched for all pairs of proteomes, running both passes in parallel. When both passes are finished, their outputs are validated by checking for truncation or failure to complete. Intra-proteome matches are checked against the proteome sequences to ensure inclusion of all genes. Pass 1 pairs are combined with pass 2 results such that only pairs accepted in pass 1 are kept, but with alignments from pass 2. A failed validation will either lead to a whole proteome rerun for failed/truncated results or individual serial pass2 reruns for pass1 pairs lacking pass2 results.