how to annotate any sequence using Sequence Ontology

Question

[solo7773]

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Hello everyone. I just find the Sequence Ontology (SO, http://www.sequenceontology.org) is really great. I want to annotate my sequence using it but don't know how to. For example, I have a sequence of somatic deletion,

chr    start    end    type    seq
chr11    67077296    67077312    deletion    CACAGTGCTGGCCTATG

I want to map it to a term of children of SO:0000159. Does anybody know how to achieve this? I have thousands of mutations. If one can provide a hint, I am able to hack this.

I find there is a tool named Genome Annotation Library (GAL) developed by the SO team but I haven't learnt to use it so I am not sure if it will work for me. I also know Variant Effect Predictor (VEP) from Ensembl can predict consequence of this mutation to a SO term but this is not what I need.

I really appreciate if one can offer help. Thanks in advance.

Answer 1

[Denise CS]

Use the Ensembl Variant Effect Predictor. There is the VEP script, web interface and Variation REST call. It will assign the SO terms to your variants. You can use the VEP for any type of variants including deletions to get them annotated (e.g. missense, stop loss, inframe deletion, etc).

[solo7773]

Hi Denise, thanks very much.