tool: changes in binding affinities caused by SNP

Is there any tool which as input takes two sequences: one with snp and another without and calculates the differences in the binding affinities using jaspar (as a bash or r script)?

snp

• 1,653 views • link

updated 4.2 years ago by Ram

• written 11.4 years ago by tonja.r

0 answers

No answers yet.

More posts like this

Tools to visualize 2D RNA Heterodimer
written 4.5 years ago by nhaus •

Hello, I am currently predicting RNA structures using [RNAcofold][1]. I was wondering if any of you know a tool (preferably in R) which can be …
Online BLAST search using R
written 5.0 years ago by accibio •

Is there a way to incorporate online BLAST search using an R script which takes FASTA sequences as input and returns the BLAST hits?
Salmonella Typhimurium Strain Lineage
written 6.4 years ago by Fid_o •

I have 900 assembled Salmonella Typhimurium ST313 sequences (.FASTA files, average sequence size 4.7MB). Basic information says there are two lineages of salmonella strains - …
How can I find exclusively present genes between two genomes
written 8.9 years ago by adeena_hassan •

Assalam o alaikum everyone, I have genome sequences of two closely related mammals (carnivores). I want to find genes which are exclusively present between two …
tool for calculating the path length between to GO terms (in the MF aspect)?
written 10.2 years ago by halmubaid •

Hi, Is there any software (or online tool) that calculates the path length between two GO terms?
exome sequencing, target capture
written 11.7 years ago by tonja.r

Hello, I have some problems with the understanding of the part of exome sequencing where the targets (exons) are captured. And how the SNPs (or …
By using JASPAR API and PWMScan which tool is more accuracy to predict transcription factor binding…
written 12.1 years ago by michaelchen33 •

As title. I am using JASPAR data: MA0058.2(transcription factor: MAX) to scan whole genome(hg19), I found out that JASPAR has already did the job and …
Rna Base Paring
written 12.9 years ago by layal •

Is there any program that takes as an input two RNA sequences and tells you as an output which regions from both sequences possibly base-pair …
Get Snp Position From A Python Interface.
written 13.6 years ago by Peixe

Hi, I have a Python script which takes as input a list of SNPs, then calls <a href='http://samtools.sourceforge.net/tabix.shtml'><code>tabix</code></a> to retrieve .VCF file and does some …
Calculating Z-Scores
written 14.7 years ago by Diana

Hello everyone, I have a set of sequences in which I am identifying over-represented transcription factor binding sites. I've used Patser to identify all possible …