Questions tagged [dna]
Acronym for deoxyribonucleic acid, the unit of inheritance for all eukaryotic and prokaryotic organisms
98
questions
3
votes
1answer
65 views
Why does the SARS-Cov2 genome has letter t
ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC TTTCGAT... is genome of an RNA virus SARS-Cov-2.
RNA contains letters C+...
-1
votes
1answer
26 views
What is meant by transcriptional changes executed by the cell over a time period?
I read the following line in the research paper - The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells:
During differentiation, for example, each ...
1
vote
1answer
49 views
Translate all reads in a .fastq into protein sequence from deep mutational scanning experiment
I'm working with paired-end NGS reads from an Illumina platform. The sequences I have are all of the same gene, but have one or more substitution mutations each.
Here is a rough workflow for ...
1
vote
1answer
14 views
Encoding different DNAs in pySBOL3?
I want to encode two different DNAs using pySBOL3. First dna is an engineered region usually composed by a transcriptional unit (TU) or a set of TUs. The second is vector which is a basically a ...
0
votes
0answers
43 views
How likely is it to find primers sequences in already-trimmed reads?
So, I am analysing 18S amplicon data (fastq files) to be able to eventually investigate the taxa composition.
After removing primers (using cutadapt) from both R1 ...
0
votes
1answer
29 views
How to know if the DNA sequence has been assembled and why is it important to know how it was assembled?
I have downloaded my FASTA format files, that have the DNA sequences of the coding region of the genes and the DNA sequence of the complete genome, from NCBI. How can I recognize if these sequences ...
1
vote
1answer
30 views
Output of allelic association doesn't write the rsID
I'm using plink (1.9b5) to do allelic association. My problem is that my output does not write the rsID (SNP), it just writes a dot.
Output:
...
1
vote
2answers
69 views
How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?
I need to identify the sequence of a gene in the complete genome sequence . I thought it was simple, instead it is not a straightforward task !
My method was the following: I downloaded the FASTA ...
0
votes
1answer
41 views
How to compute a p-value for the similarity measurement of two DNA sequences/contigs?
I'm attempting to come up with a statistical model to determine the p-value for the similarity value $ 0 \le s \le 1 $ of two DNA contigs.
The idea is to get a numerical measure to estimate if two ...
1
vote
0answers
15 views
How to interpret complete genome sequence in NCBI
I have a very basic and quick question: does the complete sequence of nucleotides of an organism (for example this one that I am considering in my homework of Pyrococcus Fuoriosus) reported in NCBI ...
2
votes
2answers
55 views
What is the file .mums created by mummer?
I am doing genome sequence alignment using MUMmer, in particular I want to do a dotplot with mummerplot. So the passages that I did are:
1.create a file .mums with the following command line:
...
2
votes
1answer
55 views
Shannon's Entropy and DNA
I have been working with Shannon's entropy (SE) and DNA lately, and referring to the formula and concept of SE, I just wondered whether one should in the case of DNA use each nucleotide as having a ...
2
votes
0answers
17 views
Tajima-Nei Distance estimate with BioPerl
I have been trying to estimate Tajima-Nei distance for my data (link below).
I´m following this protocol from BioPerl: https://metacpan.org/pod/Bio::Align::DNAStatistics
I have 314 sequences in a ...
1
vote
2answers
119 views
Fastq: how can I check if they are from DNA or RNAseq data?
I have (gave me) Illumina fastq files, which I want to use for variant calling, and I do not know if they are DNAseq or RNAseq data. How can I check this? I do not have any report or who to ask.
Many ...
0
votes
1answer
29 views
Dataset showing evolution of gene
As a way to exemplify how the hierarchical clustering of particular DNA sequences can be used to derive phylogenetic trees, I'm looking for a (even very small) dataset of the same genes (or other ...
0
votes
0answers
86 views
Convert DNA raw data between a different formats [duplicate]
I have .vcf file with partly decoded genome provided by some service. How can I convert this file into other popular formats which may be used in other services? I'...
2
votes
1answer
53 views
How can I use my Myheritage DNA results file for further analysis?
I had my DNA tested by Myheritage and they sent me a csv file with RSID, Chromosome, position and result (which base) with about 700,000 rows.
I understand most analyses of DNA use VCF files but is ...
-3
votes
1answer
41 views
Does anyone know how I can convert DNA code into FASTA for this TTGAAACACTGGATGAATGAAAAGCCCTGCTTTGCAACCCCTCAGC [closed]
TTGAAACACTGGATGAATGAAAAGCCCTGCTTTGCAACCCCTCAGC this is the DNA code Sequence. I have tried converting each into the amino acid and ended up with this LKHWMNEKPCFATPQX but I was told that this isn't ...
2
votes
4answers
162 views
What are the applications of DNA or RNA pattern matching? [closed]
I'm assuming we don't do pattern matching in DNA or RNA for the fun of it. So I'd like to know what are the applications of pattern matching or where does it fit in in larger applications?
I'm a ...
0
votes
0answers
42 views
Pairwise alignment using CIGAR String
I want to perform pairwise alignment and get the resulting CIGAR string.
The channel can emit insertions, deletions and substitution errors.
For example, if the input was AAGCT
Then the output could ...
0
votes
0answers
23 views
DNA sequence error annotation
Suppose I generate a DNA sequence of the following pattern.
AAGTC
And after being passed through a channel with insertion, deletion and substitution errors obtain the following sequence
AAAGGC
Where ...
0
votes
1answer
74 views
How to concatenate two fasta sequences by py
I have three backbone and i want to concatenate 70 sequence into these backbone.
such like:
fasta file 1:
...
1
vote
2answers
41 views
Multiple Alignment cost application
Is there any biological application/case where someone would be interest in the estimated total cost of the alignment between a set of sequences (genes or amino acids) without the aligned sequence ...
1
vote
1answer
46 views
Get raw genome sequence
I'm currently working on testing some matching algorithms for strings. I would like to do some tests on raw genomic data as I expect different results from random strings given the lower entropy. How ...
0
votes
1answer
108 views
Reading fasta sequence regions with faidx
Im coding in c++ and reading in different reference genomes to examine regions across the chromosomes a few hundred basepairs at a time.
To do it in c++ i use the library htslib and the command ...
2
votes
1answer
55 views
Mining documents for nucleotide and peptide sequences
The text mining literature has an emphasis on identifying and normalizing gene names, mutations, pathways, concepts, and so on. I haven't been able to find much, however, on methods for extracting ...
4
votes
1answer
119 views
Are there computational tools to extract features of DNA sequences?
I am looking for tools to extract features from short DNA sequences. For example, entropy, complexity, GC-content, etc.
I have found the generateFeatures.py script from the PyFeat repo, but is there ...
1
vote
1answer
25 views
How can I run the fdnadist command from the EMBOSS package?
My operating system is Mac OS X.
I would like to compute DNA distances between different sequences. For this, the dnadist package from the Phylip software would be good but hard to automate. EMBOSS ...
0
votes
1answer
41 views
BioJava - Protein to DNA
Using Biojava 5, I am trying to convert a sequence of Amino Acids to a Nucleotide sequence. Any idea how to do this?
6
votes
1answer
336 views
Biohackers Netflix - DNA to binary and video
I'm not sponsored or anything, just interested in their challenge to decipher their DNA code.
They encoded their first episode of "Biohackers" video/binary file to DNA code and said if we ...
0
votes
0answers
22 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 ...
1
vote
1answer
125 views
Need a alternative or more complex version of venn diagram in python for matching dna sequences
I am in google colab and I have combined and set up a data frame list of sequences that goes like this
Location ID Sequence
1.1 ........ A ........ AAGAGATA
1.2 ........ A........... ...
0
votes
2answers
57 views
How to modify DNA evolution model to fit actual data?
I'm working on understanding the evolution of a gene in a phylogenetic tree. I know the rates of evolution of each organism (from the tree).
I am taking a random DNA sequence with my gene, evolving it ...
0
votes
2answers
49 views
Transcribing DNA exons and append transcripts into a list
I am trying to find a way to read and transcribe a list of DNA sequences (list of lists) only when the for loop finds a start codon (triplet of the list items) and until it finds a stop codon, over ...
1
vote
0answers
36 views
"How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?"
I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I ...
1
vote
1answer
37 views
DiffBind, diffferentially binding site
I have data for 3 histone marks (2 for silencing and 1 for activation) each mark has three replicates.
when I run the diffBind package I have three contrast:
...
0
votes
0answers
37 views
Coding vs non-coding DNA length
I am trying to calculate the total exonic length (in bp) in order to see where the coding-noncoding ratio of roughly 1% to 99% comes from.
We know all chromosomes total about 3 billion base pairs. So ...
0
votes
0answers
99 views
Calculate Entropy for DNA Multiple Sequence Alignment in R
I am pretty new to R. So I apologize for asking maybe a very basic question.
Let's say I have a fasta file with sequence below:
...
0
votes
1answer
36 views
Encoding a 15bp DNA sequence into a shorter than 15 digits number
I have a series of 15bp DNA sequences from single-cell barcodes and I would like to encode them into a shorter than 15 digits number so that each unique 15bp DNA sequence will create a unique numeric ...
0
votes
0answers
34 views
How many markers or loci are used in forensic DNA profiling and the effect of the DNA sequencing?
I am reading the Wikipedia page on DNA profiling, specifically the STR analysis. It says the DNA profiling relies on 20 or so loci matching. It also gives an account of finding false identification. ...
0
votes
0answers
21 views
Generating taxonomic hierarchy by species/genus name
I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a ...
1
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0answers
50 views
What steps should I follow for DNA analysis, for a classification problem?
I have a bed file which contains DNA sequences information as follow:
**
...
1
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0answers
20 views
mining DNA barcodes from Genebank/BOLD per location
Is there a method to download all the sequences for a particular geographic region (Panama) for 'DNA barcode' sequences (ITS2, rbcL or trnL). Hopefully, the specimen collection location will include ...
1
vote
0answers
40 views
Is there a software that can predict protein-DNA binding?
Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. The sequence of interest is a potential transcriptional regulator, I want to ...
0
votes
1answer
37 views
How can I extract all known mutations of my BAM (or SNP/INDL files)?
I am using a Genome Explorer tool to see all the mutations on my own DNA.
My particular interest is on listing the variants and get their names/ids.
Here are a few screenshots:
You can see that ...
1
vote
1answer
52 views
How can I convert codon coordinates to genomic position?
I am looking for a given mutation in IGV, which accepts coordinates in the form of
chr<X>:<Y>
Where X is the chromosome number and Y is the base ...
0
votes
1answer
115 views
Get regions' information from DNA sequence data (bsgenome.hsapiens.ucsc.hg19)
I have a problem in R. I have the following dataSet (the first three rows shown) (the 5th number is the methylation level in its region):
...
1
vote
2answers
62 views
Is it possible to go from a digital sequence to an actual nucleotide?
I'm trying to learn about what the state of technology is at presently. It seems like we clearly can go from nucleotide to digitally stored sequence, but can we transcribe something from the digital ...
1
vote
1answer
87 views
Problem with classification model of genomic data: every machine learing model predicts wrongly almost always the same subset of dataset
First of all, I'd like to apologize for any spelling or grammar mistakes.
I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
1
vote
0answers
38 views
Unmapping Alternative reads in BAM file
I want to do some HLA typing, most of the tools require the bam file is aligned to primary genome without alternative read handling. From the International Genome Sample Resource project, I can get ...
