Table 1 Available cancer missense mutation prediction tools
Toola | User interface | URL | User input | Highlights | Output |
|---|---|---|---|---|---|
CHASM [4] | Stand-alone software, website | http://wiki.chasmsoftware.org/index.php/Main_Page and | Genomic coordinates in space or Tab-delimited format. RefSeq, CCDS or Ensembl identifiers, together with the respective aminoacid change | Passenger mutation rate information is available for specific types of cancer | Gene annotation CHASM score COSMIC annotation |
CanPredict [5] | Website | http://research-public.gene.com/Research/genentech/canpredict | Protein sequence and a list of amino acid changes or A list of RefSeq accession identifiers with amino acid changes | Users can simultaneously analyze various combinations of mutations in a single proteinsequence Batch submission is available only with protein RefSeq identifiers | Impact prediction SIFT score and alignment Pfam domain and GO analysis |
transFIC [6] | Web service, stand-alone, website | Genomic coordinates or Protein coordinates | Users can upload up to 300 mutations at a time and run up to 20 jobs (on the website) | Gene annotation Transformed prediction scores from SIFT, PolyPhen-2, MutationAssessor and CHASM COSMIC and/or dbSNP annotations | |
MutationAssessor [7] | Website, Web API | Genomic coordinates or Protein coordinates | Users can analyze a list of mutations (on the website) Batch submission is available | Functional Impact score Link to three-dimensional protein structure UniProt and RefSeq identifiers Cancer Gene Census and COSMIC annotations Gene and protein domain annotations | |
MuSiC [8] | Stand-alone | Mapped reads from a set of tumor and normal sample pairs in BAM format Predicted or validated SNVs and indels from the cohort in MAF format Regions of interest to users (such as exon-intron boundaries) in BED format Any available clinical information | Users can analyze whole genomes and/or exomes | Significantly mutated genes and/or pathways Annotations for known databases Links mutations to user-provided clinical information |