Difference between revisions of "Mutation effect on sites (analysis)"
From BioUML platform
(Automatic synchronization with BioUML) |
(Automatic synchronization with BioUML) |
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| Line 1: | Line 1: | ||
;Analysis title | ;Analysis title | ||
| − | :[[File: | + | :[[File:Mutations-Mutation-effect-on-sites-icon.png]] Mutation effect on sites |
;Provider | ;Provider | ||
:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
;Class | ;Class | ||
| − | :{{Class|ru.biosoft.bsa.analysis.MutationEffectOnSites}} | + | :{{Class|ru.biosoft.bsa.analysis.maos.MutationEffectOnSites}} |
;Plugin | ;Plugin | ||
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]] | :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]] | ||
==== Description ==== | ==== Description ==== | ||
| − | Find transcription factor | + | Find transcription factor binding sites affected by mutations. |
==== Parameters: ==== | ==== Parameters: ==== | ||
| Line 18: | Line 18: | ||
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected | ** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected | ||
* '''Profile''' – Predefined set of site models | * '''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 | * '''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 gain track''' – Resulting track with site gain events | ||
* '''Site loss 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 | * '''Summary table''' – Summary table giving site model frequencies per mutation | ||
[[Category:Analyses]] | [[Category:Analyses]] | ||
| − | [[Category: | + | [[Category:Mutations (analyses group)]] |
[[Category:ISB analyses]] | [[Category:ISB analyses]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Latest revision as of 18:15, 9 December 2020
- Analysis title
Mutation effect on sites
- Provider
- Institute of Systems Biology
- Class
MutationEffectOnSites- Plugin
- ru.biosoft.bsa (Bio-sequences analyses plugin)
[edit] Description
Find transcription factor binding sites affected by mutations.
[edit] 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
