Find a gene of interest in a species. I have a gene of a model animal for example (a certain gene in zebrafish), and I want to get this coding region (cds) of all fish for molecular evolution analysis. Due to the presence of introns, blasting the genome results in multiple hits (blast hits per exon). I need to manually adjust each hits and get the cds area I want, I want to ask if there is an easy way to achieve what I want.
Through a cds region, the corresponding cds region is obtained in the genome of the species of interest.![enter image description here][1]


  [1]: /media/images/1a429411-4ee9-42c4-8632-fb1c9ab2
Easy is mostly relative to your skills, it is not trivial to do right though. Rule of thumb: the more conserved the protein sequence, the easier it becomes. For high sequence identities e.g. over 50% any approach is likely to work fine. 

Easy: find orthologous sequences in fish species by using web-blast and extract the sequences of blast hits (given defined cut-offs) directly from GenBank. These will often be from predicted protein-coding sequences, which is fine if the annotation is at least half-reliable. This is all possible via the web-interface.

Easy: Extract orthologues via Ensembl's compara interface (gene tree) for the gene of interest. That will give you some orthologues, but only those in Ensembl

Intermediate: get the CDS instead of protein sequences or do the same on the commandline

Harder: if you want to include badly or unannoated genomes, you can use exonerate in est2genome or protein2genome mode. That may work well for well-conserved proteins. You can use your blast results to restrict contigs to search because exonerate alignment will be much slower than a blast run.

The following command will get you the CDS sequence:

       exonerate --model protein2genome -q query.faa -t target.fna --refine full --ryo ">%qi vs. %ti %td  %m aln.length: %qal score: %s %%-ident: %pi %%-sim: %ps strand: %tS  CDS sequence \n%tcs"


Hardest: Annotate the unannotated genomes from scratch using MAKER2, BRAKER, etc. but I do not recommend it. The result for any single protein may not be better than the previous alternative.