Questions tagged [motifs]
Physically linked short region of DNA or most notably amino acids which characterise a 'pattern' identifyable by optical analysis.
24
questions
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1answer
40 views
Why does randomized motif search work?
I'm looking for intuition for why a randomized motif search works. My current thinking is as follows:
We are selecting many random kmers from our DNA sequences. The chosen kmers will bias the profile ...
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0answers
14 views
Why use shuffled input-sequences as background of MOTIF discovery? (from CLIP-seq data using MEME-suite)
By default, STREME (MEME-suite) uses second-order shuffles of the input sequences as background. STREME highlights its usefulness for CLIP-data, which would be my origin of sequence-inputs. In this ...
2
votes
1answer
40 views
How to deal with wildcards (N) in sequence logos
This is an open question that came to my mind recently, though it might be that it is not a common use case. The purpose is to find common patterns in a collection of sequences by representing the ...
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0answers
19 views
How to identify specific motif for chip-seq data
For chip-seq data, I had analyzed the samples until motif discovery using both cluster profiler and Homer for each histone mark. I was wondering what is the efficient method to determine if each GO ...
1
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1answer
31 views
How to get matching pattern along with ID in a single command in grep?
I have a file containing multiple fast sequneces. For a specific consensus pattern as input, I extracted all the matching patterns from target fasta sequences with
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1
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2answers
88 views
biopython-motifs , How can I create motif from sequences of different length?
I want to create motif of different length kmers.
Following code works for kmers of same length but not different length.What to do ?
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0
votes
3answers
376 views
Finding motifs: fasta file with 10,000 sequences
I am new to Python. I am trying to parse a fasta file containing 10,000 sequences to look for motifs (microsatellites in particular). I tried using Seq Utils to parse my sequences for a particular ...
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0answers
30 views
Greedy Motif Search [ Reasoning ]
I was able to execute the algorithm correctly. But I'm still trying to get a hold of the result I'm achieving.
This is the algorithm I'm trying to understand -
http://rosalind.info/problems/ba2d/
If ...
2
votes
1answer
109 views
Human Herpes Virus, fusion motif in protein vs. SARS-CoV-2?
Is it possible that the fusion with cell propriety of Human Herpes virus, I see X14112.1 in GenBank is due to protein UL36 (tegument of virus) starting in linear position 2685 ???
...
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0answers
35 views
MEME's motifs have an E-vaue too high
I'm currently learning how to use MEME-Suite (web tool) to find a specific known transcriptor binding site in the promoter region of 5 putative bacterial genes of interest, but the results obtained ...
2
votes
0answers
44 views
Profile HMM to find sequence motif using Baum-Welch instead of using a given multiple sequence alignment?
I know this can be very problem-specific -- but it seemed to me the standard approach to train an HMM to recognize a binding pattern of a protein is to use the multiple sequence alignment (MSA), ...
3
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2answers
4k views
Python - Finding a motif - input: a txt file with 10 sequences and 10 motifs
When I run my BruteForce function with only one input it works and the result is correct.
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3
votes
1answer
70 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 ...
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0answers
16 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 ...
1
vote
1answer
124 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
1k 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 ...
1
vote
1answer
123 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)
2
votes
1answer
167 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 ...
3
votes
1answer
182 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 (...
7
votes
1answer
1k 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 ...
4
votes
2answers
747 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
487 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 ...
4
votes
2answers
276 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 ...
8
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3answers
156 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 ...