Thank you for the valuable links. All approaches seem to be good, and I'm checking three links to serve my purpose.
Again, thank you for your comments.
I would like to count gene copy numbers of my gene list (more than 100 genes) in mammals (human, mouse, cow, etc.). For example, I want to know evolutional copy number changes of TP53, but I don't come up with an efficient solution.
Do you have any idea to count gene copy numbers systematically?
Thanks
NCBI Homologene has the alignment information available for Euteleostomi for TP53: https://www.ncbi.nlm.nih.gov/homologene/460
Ensembl has a number of comparative genomic analyses available (scroll down to the bottom of page): http://useast.ensembl.org/Homo_sapiens/Gene/Compara?db=core;g=ENSG00000141510;r=17:7661779-7687550
A table with orthologs from multiple species can be found here (scroll down the page) : http://useast.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000141510;r=17:7661779-7687550
Thank you for the valuable links. All approaches seem to be good, and I'm checking three links to serve my purpose.
Again, thank you for your comments.
Use the most efficient solution of all: use the work done by someone else. For example, look at the OrthoDB report for TP53 at mammalian level of clustering:
https://www.orthodb.org/?level=&species=&query=125711at40674
If you scroll down to Orthologs by organism and click-select the Show all available species, you can see which species have duplications of the gene in question. You can also download the information as a tab-delimited file, which is then easily parsed to get the information you want:
pub_og_id og_name level_taxid organism_taxid organism_name int_prot_id pub_gene_id description
125711at40674 Cellular tumor antigen p53 40674 9305_0 Sarcophilus harrisii 9305_0:003593 TP53 Cellular tumor antigen p53
125711at40674 Cellular tumor antigen p53 40674 9361_0 Dasypus novemcinctus 9361_0:00312e TP53 cellular tumor antigen p53
125711at40674 Cellular tumor antigen p53 40674 9365_0 Erinaceus europaeus 9365_0:0002dd TP53 Cellular tumor antigen p53
125711at40674 Cellular tumor antigen p53 40674 9371_0 Echinops telfairi 9371_0:000064 LOC101647784 LOW QUALITY PROTEIN: cellular tumor antigen p53-like
125711at40674 Cellular tumor antigen p53 40674 9371_0 Echinops telfairi 9371_0:00380f TP53 cellular tumor antigen p53
Finally, OrthoDB provides an API which can be used with curl or wget, this allows automation for the case of several genes. I never used it, though, so I can't provide guidance here.
Another source could be OMA.
"Use the work done by someone else." I was impressed by your philosophy.
Also, your approach is appropriate for my purpose. I'm trying it using my genes.
Thank you for your valuable comment.
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Hi , Maybe you can get the fasta list corresponding to your genes of interest and blast it against mammals in NCBI.
Best
I’ve always use NCBI using specific organism names. Thank you for your valuable comment.