Orthologous Versus Clustal Scores?

Question

[Stephanhart]

I am interested in a poorly characterized human gene. When I search for orthologues in Ensembl, I get a target ID = 96% and query ID = 96% for marmoset. However, when I do a ClustalW2 analysis I get a score of 67 for marmoset. Are these scores inconsistent? What is the target ID compared to the clustal score? I'm grateful for any information.

Thanks Stephan

[Leszek]

you align nucleotides or proteins?

Answer 1

[scapella]

Hi Stephanhart,

I don't get how you make your orthologs search but if you have used BLAST to make your search then the differences you got is because BLAST is using a local alignment strategy while CLUSTALW2 is using a global alignment strategy. Having that in mind, you can expect to have a lower global identity score between two sequences than a local identity score for a particular fragment of your gene.

I hope this makes sense to you.