IconPrediction UCSC0 ×

Node extension for KNIME Workbench version 1.0.24 by Pierre Lindenbaum

Variant effect predictor using the UCSC KnownGene table.
The mysql database MUST contain a copy of the UCSC KnownGene table. (eg: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz)
Note for IRT/nantes users: use port 3316 in the JDBC uri

References

Knime4Bio. Author: Pierre Lindenbaum PhD, INSERM UMR 915, Institut du thorax, Nantes. Reference: manuscript in preparation. Please, report any problem here.

Options

jdbc.uri
JDBC uri. For the ucsc mysql sever it is:
jdbc:mysql://genome-mysql.cse.ucsc.edu/hg19
jdbc.user
JDBC user. For the ucsc mysql sever it is: "genome"
jdbc.password
JDBC password. For the ucsc data it is empty
CHROM
chromosome column
POS
Position column (first base is 1)
REF
REF column
ALT
ALT column
genome reference
Full path to reference genome indexed with samtools faidx
mRNA
add mRNA sequence
protein
add protein sequence

Input Ports

A VCF-like table (CHROM/POSITION/REF/ALT)

Output Ports

Annotated VCF containing the predicton of the consequences of a mutation (wild AA, mutated AA, position in protein , etc...)

Update Site

To use this node in KNIME, install Node extension for KNIME Workbench from the following update site:

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