Welcome to the OncoMiner Pipeline

Click SUBMIT to submit a nucleotide variant file to the pipeline for processing.

This server allows you two upload two kinds of files:
  1. Nucleotide variant files in the format described below, typical of Otogenetics exome-sequencing results, which will be processed by the pipeline to provide PROVEAN scores and PubMed cross-references.
  2. Gene-list files, which can be used to restrict the processing of nucleotide variants to specific genes, and/or to exclude specific genes from being processed.

A submitted job will produce four output files:

  1. jobname.PROVEAN.csv: contains rows of the same format as the input file, except that each row is duplicated for each isoform of the affected protein, and columns indicating the AA variant in Human Genome Variation Society format, the PROVEAN score for the specific isoform variant (as compared with the GenBank human genome reference assembly, build 37), BBRC FASTA header name, and protein length.
  2. jobname.summary.csv: contains rows of the same format as the input file, with one row per input row. Additional columns are added indicating the minimum and maximum PROVEAN scores for any isoform resulting from the variant; and a column is added containing all isoforms' PROVEAN scores separated by vertical bars.
  3. jobname.annotated.csv: this file is in the same format as the jobname.PROVEAN.csv file, except that additional columns indicating the Gene Ontology terms associated with each row's gene name, and hyperlinks to any PubMed references that were found for the dbSNP or HGVS variant, are added. Also, rows with high (non-damaging) PROVEAN scores are omitted.
  4. jobname.PROVEAN.full.annotated.csv: This is like the jobname.annotated.csv file, except it contains all rows; no filtering by PROVEAN score is performed.
Click here to see a specification of the required format of input files.

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