Thibault Robin, a PhD student in our group, has developed a very powerful STR similarity search tool that was made publicly available a few weeks ago:
With this tool you can search for similarities between your cell line samples and the human cell lines STR profiles stored in the Cellosaurus. Highlights of this tool are the following:
- It accepts all STR markers that have been used for authentication (31 different markers + amelogenin).
- You can select between 3 algorithms: Tanabe (https://doi.org/10.11418/jtca1981.18.4_329) and two versions of the Masters (https://www.ncbi.nlm.nih.gov/pubmed/11416159) algorithm.
- You can define search modes: deciding if amelogenin is taken into account or not and how the program treats empty markers in the query sample or in the stored STR data.
- The results are displayed in a user-friendly tabular format that can be exported as a file (CSV, JSON or PDF formats).
- If you wish to search for similarity to multiple cell line samples you can do so by using the "batch mode", i.e. by specifying a file that contains the STR marker information for the cell lines.
- It can be accessed programmatically through a RESTful API. The documentation for the API is found in the help page: https://web.expasy.org/cellosaurus-str-search/help.html
In addition to being available on the Cellosaurus home page, the tool is accessible from any human cell line entry that contains a STR profile and will search for similarity to that profile.