Additional File 4.

Channel catfish proteins and ESTs identified using the ProtIDer tool. The ProtIDer tool is designed for use with species that have large numbers of ESTs but few proteins in the NRPD. ProtIDer matches ESTs and EST assemblies to highly homologous proteins from other species by TBLASTN-searching the NRPD with all catfish ESTs. For example, the channel catfish genome sequence is not available and there are only 1,108 NRPD entries for this species. When we analyzed channel catfish ovary tissue we were only able to identify 10 proteins from NRPD. Using ProtIDer to create a database of highly homologous proteins resulted in a five-fold increase in the number of proteins identified in this experiment. The proteins identified from the channel catfish NRPD database (cfNRPD), highly homologous database (hpDB) and EST databases are shown here. The ProtIDer tool is available from AgBase upon request.

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McCarthy et al. BMC Genomics 2006 7:229   doi:10.1186/1471-2164-7-229