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Questions tagged [motifs]

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1
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1answer
25 views

De novo motif discovery in protein sequences

I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a ...
0
votes
0answers
15 views

Finding gene name from human genome using SP1 transcrition factor binding site from Postion Weight Matrix

I have a list binding site motif of SP1 transcription factor which collects from PWMScan tools. Actually this tool scan whole human genome and give the entire binding motif list. From that list of ...
0
votes
1answer
39 views

Motif Discovery in Bipartite networks using Cytoscape

I am trying to find over-expressed motifs in a bipartite transcription factor gene network.My genes are not very well characterized, so finding functional motifs has been a challenge. I used the motif-...
14
votes
1answer
185 views

Biopython Phylogenetic Tree replace branch tip labels by sequence logos

Having recently constructed a lot of phylogenetic trees with the module TreeConstruction from Phylo package from Biopython, I've been asked to replace the branch tip labels by the corresponding ...
0
votes
1answer
64 views

Creating frequency plot from weblogo with frequency unit on the Y axis

Hello I am trying to create frequency plot for a motif with frequency unit on the Y axis from 0 -100 nt as the unit as represented in this paper.(Seiler et al., 2018)
3
votes
1answer
57 views

Searching for protein motifs with MEME

I am trying to look for motifs in a set of proteins returned by a mass spec experiment using MEME. The experiment was carried out in the yeast Candida albicans. Does anyone know if it is worth ...
2
votes
1answer
43 views

Database of position weight matrices for protein motifs?

I am trying to identify proteins that carry a consensus target sequence for a kinase. Usually if I am working with, for e.g. transcription factors binding to DNA I would use position weight matrices (...
5
votes
1answer
171 views

Where to download JASPAR TFBS motif bed file?

I am interested in determining if any transcription factor binding site motifs are enriched in some BED files from a DNA methylation experiment. I am looking for a database that has BED Files ...
3
votes
2answers
227 views

Where are .motif files from homer knownResults?

I have been using homer's findMotifsGenome.pl, but with my new version (v4.9.1) of homer I don't get ...
7
votes
5answers
228 views

What motif finding software is available for multiple sequences ~10Kb?

I have around ~3,000 short sequences of approximately ~10Kb long. What are the best ways to find the motifs among all of these sequences? Is there a certain software/method recommended? There are ...
3
votes
2answers
98 views

How to calculate statistical significance of sequence motifs

I would like to show that certain types of RBP motifs are enriched in RNA editing islands (i.e. clusters of RNA editing). However, I am unsure about how to think about sequence motifs with respect to ...
7
votes
3answers
87 views

Have DNA motifs 6-12bp long, trying to get conservation scores

I have about 200 short nucleotide motifs (6-12 bp in length) from the human genome, and I'm trying to see how conserved they are across vertebrates. I was thinking that I'd need to make a bed file ...