I'm trying to locate all possible copies of a particular gene that exist in the zebrafish genome and I'm having a hard time correlating the entries from distinct databases. I would like to know which is the most complete and reliable zebrafish genome database in your opinion?
I use a combination of Ensembl and UCSC genome browser. The last one has more EST sequences available (more user friendly) to compare and contrast with gene models presented by Ensembl. Best!
I would suggest using ZFIN. It is more specialised and it was made by researchers that use zebrafish as a model. You can use the other databases as well but keep in mind that some genes have different names .
ZFIN would be the best place to start and do keep in mind that the zebrafish has two copies of a great number of genes. Sox9 comes to mind as one such gene.
If your gene(s) of interest is in Genbank it is easiest to search via BLASTx using a nucleotide sequence as a query or tBLASTn using a protein query. You can search specifically for ESTs or Whole Genome Shotgun (WGS). There's plenty of little nuggets lurking in those databases if you figure out how to search them
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