Gene names from NCBI is not able to use for overlapping in species comparison
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5.6 years ago
Amk ▴ 120

Hi,

I want to check the overlapping genes between three species. I fetched all the Gene names from the GENE database of NCBI. The list had synonym names for several genes. I am confused which all synonyms should I remove before I plot Venn diagram. I fear that some synonyms may hit on the other list which can make an increase in the overlaps. If I remove the synonyms list and go with the genes names will I lose overlaps? Any Idea to make all the genes in a standard form independent to species?

Thanks in Advance,
Amk

NCBI Overlap Venn conversion comparison • 1.2k views
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5.6 years ago
abascalfederico ★ 1.1k

I guess you mean orthologous genes not overlapping. You can use phylogenetic trees, for example from Ensembl Compara, or look at Genomicus and the synteny

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Hi abascalfederico,

Thank you for your suggestion.

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