Velvet_Reference_protein_matching.txt

Sequences of our reference based on the Lucania parva velvet assembly (kmer=25) with a total of 24,781 contigs, combining 1,657 contigs from the L. goodei assembly (all unique contigs over 200bp) with L. parva contigs that had blast matches to any of the following: 1) related teleost proteomes (Atlantic killifish: Fundulus heteroclitus, Japanese medaka: Oryzia latipes, three-spined stickleback: Gasterosteus aculeatus), 2) Fundulus ESTs on the microarray, or 3) target genes of interest (osmoregulation and vision related genes). Blast results from blastX searches against the uniprot proteomes were retained only if contigs had only 1-2 protein matches per species (blast score > 100) to avoid inclusion of contigs that were misassembled from multiple genes.