Mutation effect on sites (analysis)

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Analysis title
Mutations-Mutation-effect-on-sites-icon.png Mutation effect on sites
Provider
Institute of Systems Biology
Class
MutationEffectOnSites
Plugin
ru.biosoft.bsa (Bio-sequences analyses plugin)

Description

Find transcription factor binding sites affected by mutations.

Parameters:

  • Input VCF track – Input track in VCF format
  • Genome – Reference genome
    • Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
    • Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
  • Profile – Predefined set of site models
  • Score type – The type of position weight matrix score
  • Score difference – Minimal site score difference between reference and alternative sequences
  • Independent variations – Treat each variation independently
  • Target gene TSS upstream – When searching for target genes, match TF binding sites to this distance upstream of TSS.
  • Target gene TSS downstream – When searching for target genes, match TF binding sites to this distance downstream of TSS.
  • One nearest target gene – Report only one target gene nearest to TSS.
  • Output table – Output table
  • Site gain track – Resulting track with site gain events
  • Site loss track – Resulting track with site gain events
  • Important mutations – Track of mutations that affects binding sites
  • Summary table – Summary table giving site model frequencies per mutation
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