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Questions tagged [motifs]

Physically linked short region of DNA or most notably amino acids which characterise a 'pattern' identifyable by optical analysis.

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Help Understanding the Greedy Motif Search Algorithm from Textbook

I am trying to go through this text book on Bioinformatics: https://www.bioinformaticsalgorithms.org. It has coding challenges and problems which I hadn't had too much trouble with until I got to the ...
David Rouleau's user avatar
1 vote
2 answers
33 views

How to classify TF motifs by family

I have a FIMO output, the input sequences were putative promoter sequences of several species. I want to graph the positions of these motifs along a horizontal graph, but I want to filter the data by ...
JohnDoe23's user avatar
1 vote
0 answers
54 views

Recommendations on Motif scoring functions

I am searching for specific transcription factor binding locations on DNA, and ranking them according the their scores. For this, I am in search of a tool or method that can generate motif scores for ...
Zebra Fish's user avatar
1 vote
2 answers
101 views

How to visualize FIMO outputs?

I used FIMO to scan several of my promoter sequences for TF binding motifs. The output .tsv file gives me the motif name/sequence plus the start and stop location, how can I visualize these outputs to ...
JohnDoe23's user avatar
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0 answers
18 views

Prediction of DNA binding motif from sequence/structure of TF/regulator protein?

Do you know if it is actually possible to predict with good accuracy a DNA binding motif from only the sequence/structure of the DNA-binding protein?
Icarus's user avatar
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1 vote
1 answer
142 views

How much of the space of motifs have been discovered?

I notice when using tools like HOMER there are two different types of outputs: de novo motifs vs known motifs and it seems no matter what the data is (type of ChIP etc.) there is always a "de ...
Zebra Fish's user avatar
4 votes
2 answers
217 views

Searching motifs in sequence and their frequencies

This is a two part question. I am searching for a motif, and in that search I wanted to also find the total number of sequences in my FASTA file, but the code I wrote is not yielding that please see ...
thole's user avatar
  • 143
0 votes
1 answer
100 views

finding the frequency of a motif-matching peptide

This question has also been asked on Biostars I want to find the frequency of each motif-matching peptide. The sequences are: ...
thole's user avatar
  • 143
2 votes
2 answers
35 views

finding overlapping motifs to increase length of motif

I am able to find matching motif in my sequence, and I would like to now find overlapping motifs. Basically, after matching my motif, I want to find the 6 amino acids after it. This is the code below ...
thole's user avatar
  • 143
2 votes
2 answers
267 views

motif searching in a multi-fasta file

I am having trouble trying to search for motifs in a multi fasta file. I have used two techniques one gives me the name of the sequence where the motif is found but doesn't give me the the motif and ...
thole's user avatar
  • 143
2 votes
1 answer
230 views

finding motifs in fasta file with multiple sequences

I am able to find matching motifs on a single sequence, as well as their position as shown below : ...
thole's user avatar
  • 143
1 vote
1 answer
219 views

finding matching motifs in a sequence and their position

I am trying to find some matching motifs on a sequence, as well as the position that the motif is located in and then output that into a fasta file. The code below shows that the motif ...
thole's user avatar
  • 143
2 votes
1 answer
37 views

How to count number of motifs in Prosite?

For example I checked motifs in Transferrin P02787 https://prosite.expasy.org/cgi-bin/prosite/ScanView.cgi?scanfile=816050634835.scan.gz I have hits by profiles: [2 hits (by 1 profile) on 1 sequence] ...
MrMorgotheron's user avatar
3 votes
1 answer
192 views

heatmap of specific sequence motifs in aligned fasta files

I have a collection of fasta files, each containing three aligned sequences. I am interested in understanding the distribution of a specific sequence motif PGP, RGP and KGP in all the alignments. I ...
Jalan's user avatar
  • 31
1 vote
2 answers
71 views

Tool for cross referencing a newly found MOTIF to database of known MOTIFS

I need a tool or a function I can use in my code (R, or Python) that I can cross reference a MOTIF against known MOTIFS, a function that will take as input a MOTIF (a probability weight matrix, PWM ...
Zebra Fish's user avatar
2 votes
2 answers
507 views

PWM (4xM matrices) to Sequence Logo Visualizations in MATLAB or Python

Is there a MATLAB, or else Python (not R) tool for visualizing sequence Logos from probability weight matrices (PWMs)? This seems like a basic and simple tool to implement, yet just above the ...
Zebra Fish's user avatar
0 votes
1 answer
114 views

Heatmap of motifs present in protein sequences

I have a file containing multiple protein amino acid sequences. I am interested in visually presenting the location of amino acid motifs PQG, QQG and AQG in the sequence in the form of a heatmap in R. ...
Jalan's user avatar
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1 vote
0 answers
27 views

How do I intrepret the generated motifs of a dataset of 5-methylcytosine (5mC) sequences?

I'm a computer science person currently working on a project which uses deep learning to identify 5mC sites of Nipponbare Rice. Within the project, there is an option to view what the model 'discovers'...
EnigmaticCocoon's user avatar
2 votes
1 answer
111 views

Where to get BED files for regions that contain binding site motifs for specific transcription factors?

Quick question, is there a place where one can download BED files for the binding motifs of certain transcription factors. In my case, I'm looking for a BED file for the genomic regions (enhancers) ...
user305902's user avatar
1 vote
1 answer
454 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 ...
Moo's user avatar
  • 127
2 votes
1 answer
48 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 ...
Álvaro's user avatar
  • 143
0 votes
0 answers
29 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 ...
Mariam's user avatar
  • 115
1 vote
1 answer
132 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 ...
20 21's user avatar
  • 13
1 vote
2 answers
301 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 ? ...
Lipsa's user avatar
  • 21
0 votes
3 answers
844 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 ...
ShawnC's user avatar
  • 31
0 votes
0 answers
130 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 ...
zion's user avatar
  • 101
2 votes
1 answer
115 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 ??? ...
RosLuP's user avatar
  • 215
1 vote
0 answers
48 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 ...
Laura Pineda's user avatar
2 votes
0 answers
48 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), ...
skc's user avatar
  • 43
3 votes
2 answers
5k 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. ...
Beeta's user avatar
  • 31
3 votes
1 answer
114 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 ...
wrong_path's user avatar
1 vote
0 answers
21 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 ...
nayan de's user avatar
1 vote
1 answer
161 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-...
The Last Word's user avatar
14 votes
1 answer
2k 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 ...
Boris Schnider's user avatar
1 vote
1 answer
217 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)
AishwaryaKulkarni's user avatar
2 votes
1 answer
227 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 ...
Ian Sudbery's user avatar
  • 3,321
3 votes
1 answer
263 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 (...
Ian Sudbery's user avatar
  • 3,321
7 votes
1 answer
2k 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 ...
Reilstein's user avatar
  • 367
4 votes
2 answers
1k 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 ...
benn's user avatar
  • 3,571
7 votes
5 answers
607 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 ...
ShanZhengYang's user avatar
4 votes
2 answers
362 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 ...
tweirick's user avatar
  • 171
8 votes
3 answers
168 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 ...
Eric Brenner's user avatar