Table 5

Reciprocal BLAST comparison between catfish and five model fish with sequenced genome
Species #Total proteins #Protein coding genes #Proteins have hits in catfish #Genes have hits in catfish #Unique protein hits by catfish #Unique gene hits by catfish
zebrafish 40,585 26,152 39,250 25,330 24,281 20,014
fugu 47,841 18,523 47,583 18,336 26,230 15,834
medaka 24,661 19,686 23,311 18,465 18,200 16,007
stickleback 27,576 20,787 26,375 19,740 19,503 16,835
Tetraodon 23,118 19,602 22,648 19,208 17,636 15,996

First, protein sequences of five model fish in Ensembl database were searched against catfish contigs using TBLASTN to assess the extent of reference sequences that were observed in catfish; reciprocally, all catfish contigs were searched against protein sequences of five model fish using BLASTX to assess the number of genes represented by the catfish sequences when compared to those in each of the five species.

Liu et al.

Liu et al. BMC Genomics 2012 13:595   doi:10.1186/1471-2164-13-595

Open Data