Mutalyzer 3.0 API

[David Atlan]

Hi,

we are using the 'runMutalyzer' command of the API from 2.0, for example:

https://v2.mutalyzer.nl/json/runMutalyzer?variant=NM_000384.3%3Ac.10580G%3EA

I have looked at the list of the API from 3.0 here:

https://mutalyzer.nl/api/

but can't find this command, is it still to be implemented, or did it change its name?

Thanks a lot,

David

[Mihai Lefter]

Hi David,

Thanks for using Mutalyzer.

In Mutalyzer 3 you can make use of the "normalize" endpoint:

https://mutalyzer.nl/api/normalize/NM_000384.3%3Ac.10580G%3EA

Please note that the response is also different.

Best regards,

Mihai

[David Atlan]

Hello again,

thanks for your quick previous response! We have started to implement the changes on our side to call the v3 API. There are two functions from the old API that I can't find in the new one:

1. is there a way to get the nucleotide sequence? We used this function to generate something like:

agctggattg[A/G]agctagca

(something like the "View variants sequence info" field in the web interface would be great)

for a variant to be able to call the online MutationTaster tool.

2. is there a way to get the genomic position of a variant (from a c. position and transcript)? Either on hg19 or hg38?

For NG_009060.1, transcript NM_000527.4, there seems to be NM_000527.5 on NCBI, but not yet in Mutalyzer, will you be updating soon?

Thanks a lot for your help,

Best wishes,

David

[Mihai Lefter]

Dear David,

1. Could you please detail why isn't the view variants endpoint [1] suitable for your use case?

2. You can make use of [2] and check for "chromosomal_descriptions". Next, use [3] and check for "g" under "equivalent_descriptions". If in the first normalization there are no "chromosomal_descriptions", then there are differences between the NM and the NC sequences [4]. You can then use the mapper [5], to accommodate for those differences.

Let me know if you have any other questions.

Best regards,

Mihai

[1]: https://mutalyzer.nl/api/view_variants/NM_000527.5%3Ac.100del

[2]: https://mutalyzer.nl/api/normalize/NM_000527.5%3Ac.100del

[3]: https://mutalyzer.nl/api/normalize/NC_000019.10(NM_000527.5)%3Ac.100del

[4]: https://mutalyzer.nl/normalizer/NM_032790.3:c.274A%3ET

[5]: https://mutalyzer.nl/mapper?description=NM_032790.3%3Ac.274A%3ET&reference_id=NC_000012.12&selector_id=NM_032790.3&slice_to=transcript

[phenos...@gmail.com]

Dear Mihai,

thanks for the view_variants endpoint, it works for one of our use cases, namely calling MutationTaster, but for our second use case, splice site predictions, I would need longer sequences before and after the variant, something like 70-100 nucleotides, the current returned sequence is to short for a meaningful splice prediction. Is there a way to get a longer sequence? 

For 2. I still need some time to implement and test it.

Best regards and a nice weekend,

David