Syntenator: Multiple gene order alignments with a gene-specific scoring function

Additional file 3:

Brief description of the Blockfinder implementation. This text document overviews our Blockfinder implementation, which we used as a reference implementation of a generic approach to merge information from two or more primary graphs.

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Additional file 1:

Resolving EnsEMBL 1:many and many:many orthologs. This table shows how many ambiguous pairwise orthology relations as defined by the EnsEMBL pipeline could be resolved with Syntentator.

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Additional file 2:

Supplementary Tables. Table 1 – BLASTP Homologs. Amount of genes for which BLASTP homologs could be detected (E-value < 0.1). Table 2 – One-one orthologs. Amount of Ensembl40 one-to-one orthologs which were recoverved by Syntenator. Table 3 – Overlap between syntenic blocks. For each pairwise comparison and each method, the ratio between sequence in overlapping blocks and total sequence in blocks is shown. Table 4 – Comparison of conserved synteny predictions for genome pairs. BF stands for Blockfinder. BRH denotes Best reciprocal BLAST hits. Genome data and compara data were retrieved from the EnsEMBL database release 40.

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