SNVBox Tutorial

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Revision as of 02:33, 6 November 2010 by Andywong86 (Talk | contribs)
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Preparing the requisite files

  1. SNV-Box accepts protein-based mutations. Prepare a tab delimited ".tmps" text file of your mutations in the following format:
    NP_001135977	R641W
    NP_835455	R151C
    NP_055645	L590V
    NP_689808	D28H
    NP_005472	S372R
    NP_112493	S35R
    NP_859061	A118V
    NP_892018	R153C
    NP_001074003	R264Q
    NP_001073893	R1272C
    NP_808882	R30H
    ...
    


    Currently support Refseq, CCDS, and Ensembl accessions.

  2. SNV-Box accepts a list of custom features. Prepare a text file with the list of features you want:
    ExonConservation
    ExonSnpDensity
    ExonHapMapSnpDensity
    HMMRelEntropy
    HMMEntropy
    HMMPHC
    MGARelEntropy
    MGAEntropy
    MGAPHC
    PredRSAB
    PredRSAE
    PredBFactorF
    PredBFactorS
    PredSSC
    PredSSE
    PredSSH
    AAHydrophobicity
    AAVolume
    AAPolarity
    ...
    

Retrieving features

  • To retrieve features from a single mutation file:
    > SNVget -f [feature list file] -o [output arff file] [mutation file]
    
  • To retrieve features from multiple classes the file names as class labels:
    > SNVget -f [feature list file] -o [output arff file] [mutation file 1 as class 1]
      [mutation file 2 as class 2] etc.
    
  • To retrieve features from multiple classes with custom class labels:
    > SNVget -c -f [feature list file] -o [output arff file] [class 1] [mutation file 1]
      [class 2] [mutation file 2] etc.
    

Available Features

  • ExonConservation
  • ExonSnpDensity
  • ExonHapMapSnpDensity
  • HMMRelEntropy
  • HMMEntropy
  • HMMPHC
  • MGARelEntropy
  • MGAEntropy
  • MGAPHC
  • PredRSAB
  • PredRSAE
  • PredBFactorF
  • PredBFactorM
  • PredBFactorS
  • PredStabilityH
  • PredStabilityL
  • PredSSC
  • PredSSE
  • PredSSH
  • AAHydrophobicity
  • AAVolume
  • AAPolarity
  • AABLOSUM
  • AAEx
  • AAMJ
  • AAPAM250
  • AAGrantham
  • AACOSMICvsHapMap
  • AAHGMD2003
  • AAVB
  • RegCompILVM
  • RegCompKR
  • RegCompWYF
  • UniprotBINDING
  • UniprotMODRES
  • UniprotMUTAGEN
  • UniprotREP
  • UniprotREGIONS
  • UniprotDOM_MMBRBD
  • UniprotDOM_RNABD
  • UniprotDOM_PostModEnz
  • UniprotDOM_LOC
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