Running Anopheles gambiae variants through VEP
We have identified seven variants in Anopheles gambiae (African malaria mosquito, PEST).
tmp_X_2058015_T_C
tmp_X_2058017_G_C
tmp_3R_6014033_G_A
tmp_3R_6014046_A_T
tmp_3L_12676608_G_C
tmp_3L_12676741_A_G
tmp_2R_39524997_G_A
Use the VEP tool in Ensembl and choose the options to see SIFT predictions. Do these variants result in a change in the proteins encoded by any of the genes? Which gene? Have the variants already been found?
Go to the Ensembl Metazoa homepage and click on the link Tools at the top of the page. Click on Variant Effect Predictor and enter the variants in the text box:
Note: Variation data input can be done in a variety of formats. See more details about the different data formats and their structure in this VEP documentation page. Click Run. When your job is listed as Done, click View Results.
You will get a table with the consequence terms from the Sequence Ontology project (http://www.sequenceontology.org/) (i.e. synonymous, missense, downstream, intronic, 5’ UTR, 3’ UTR, etc) provided by VEP for the listed SNPs. You can also upload the VEP results as a track and view them on Location pages in Ensembl. SIFT is available for missense SNPs only.
