How can I find exclusively present genes between two genomes

Question

[adeena_hassan]

Assalam o alaikum everyone,

I have genome sequences of two closely related mammals (carnivores). I want to find genes which are exclusively present between two genomes means present in one genome and absent in other. Is there any tool or perl script to find exclusively expressed genes?

[Kevin Blighe]

Masaa al-khair, my friend,

It would be helpful to have the transcriptome sequences in FASTA, because then you could compare them using a simple BLAST search, here: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome (tick the checkbox for Align two or more sequences so that you an input your second FASTA file). Transcript sequences that do not align in the other will be marked with an asterisk in the drop-down list at the top of the results page. You can then extract the sequence for these transcripts and infer possible function using BLASTx (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome).

Having the genomic sequences does not immediately give concrete evidence of which genes are expressed in one but not the other. Do you have transcriptome sequences or even any RNA-seq data?

Kevin

[adeena_hassan]

No, actually i don't have transcriptome sequence. i have two genomes one of them is published genome and other is unpublished genome which i have constructed from BAM file.

[Kevin Blighe]

I see, comparative genomics, in that case, something like VISTA could function (http://genome.lbl.gov/vista/index.shtml). Otherwise, you can always use standard BLAST to find the regions that do not match, and then run these regions through BLASTx to see if they may have any functionality in terms of proteins.

[adeena_hassan]

Thank you :) your suggestion is helpful :)

[Kevin Blighe]

No problem my friend! :)

Answer 1

[h.mon]

It seems you want to find orthologous genes between two genomes. For that, you need predicted genes from both genomes, then you could use a tool like OrthoMCL, ProteinOrtho or OMA (among others) to find orthologous genes and check which genes are exclusive for which taxa. If you have predicted genes only for the published genome, you could just blast then against the other genome and see which ones don't have a hit. If you don't have predicted genes at all, I don't see an easy way of moving forward.

I want to find genes which are exclusively expressed between two genomes means present in one genome and absent in other.

You are not searching for exclusively expressed genes. Genes present in one genome and absent in other ARE NOT exclusively expressed genes. Gene expression is one thing, gene existence is another. You don't even have expression data.

[adeena_hassan]

Thank you for correction and useful information. :)