gene prediction using gene/protein sequence from a closely related species, both organisms having sequenced genomes

Question

[fmufunda]

Hello l am trying to predict presence of a gene/protein in a closely related organism B, responsible for a known trait in organism A where it is known , l have the gene sequence as well. The organism B of interest has a whole genome shortgun sequence . Can someone help me move from gene/protein sequence to determining whether the gene/protein sequence is present in B- (orthologous/paralogous/syntenous?). Please suggest the software l can use besides having to do marker screening of populations and so on!

[GenoMax]

If the organisms are closely related then you should be able to find the homologous gene (reads) from organism B by aligning to genome A. If you have enough data then you may be able to assemble genome B and then use predicted gene translations to look in proteome of A by blast searches.

[fmufunda]

Thank you Dan quite helpful have done alignment with MEGA , blast on NCBI and getting significant coverage . Could you assist with software l can use to assemble the gene and getting predicted translations.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts. SUBMIT ANSWER is appropriate for new answers for the original question.

Since you used MEGA this must be bacterial genome (or a small genome at that). If so, look into SPAdes for assembly.

[fmufunda]

Thank you had not noticed. lts a plant genome not bacterial .

Answer 1

[DG]

You should be able to use a simple BLAST search to look for the gene of interest in your data in this case. Particularly if it is already assembled. A simple BlastN should identify it. Keep in mind that depending on the coverage and quality of the assembly for organism B that not finding the gene of interest by BLAST doesn't necessarily mean it isn't there.