Mutation effect on sites (analysis)

Analysis title

Mutation effect on sites

Provider

Institute of Systems Biology

Class

MutationEffectOnSites

Plugin

ru.biosoft.bsa (Bio-sequences analyses plugin)

Description

Find transcription factor binsing 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 difference – Minimal site score difference between reference and alternative sequences
• Site gain track – Resulting track with site gain events
• Site loss track – Resulting track with site gain events
• Summary table – Summary table giving site model frequencies per mutation