Tuesday 10 November 2015

bioinformatics - STRING ID - allelic differences and splice variants


STRING has protein (amino acid sequences) mapped to a single gene ID. I have these doubts with respect to STRING ID. I find that



1.All alleles of a single gene share the same STRING ID and


2.Especially in Eukaryotes, splice variants of the single gene(which might translate to different proteins) share the same STRING ID.




Does STRING take into account these two things like UniProt and have different IDs based on allelic differences and splice variants?If so,how?



Answer



STRING does not distinguish between different products of the same gene. E.g. for human, the protein identifier you see (ENSP...) corresponds to the longest splice form for each gene (ENSG...). Therefore, STRING won't help you if you need to distinguish between splice forms.


Splice forms are merged because for most sources of evidence, there is little data for the interactions of individual splice forms.


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