Questions tagged [dna]
Acronym for deoxyribonucleic acid, the unit of inheritance for all eukaryotic and prokaryotic organisms
101
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Generating PDB file for custom DNA sequence
I asked this question in biology.stack exchange and was referred to this community. I am going to request migration for this question.
https://biology.stackexchange.com/q/105024/67415
I want a PDB ...
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0answers
6 views
getting PDB file of interested sequence
I want a PDB file of DNA sequence I am interested in (10 base pairs) for docking. I will appreciate if any of you can please clarify some of my doubts.
Do you think, I can generate PDB file by using ...
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0answers
9 views
Why does blast produce different distance tree of results for rcbL and 18S rRNA? [closed]
question: Try to explain why the genes (rcbL and 18S rRNA) result in such differing outputs (distance of tree results) when BLAST was used? What does this mean for the use of rcbL and 18S rRNA genes ...
4
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1answer
67 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+...
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1answer
27 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
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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
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1answer
16 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 ...
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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 ...
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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
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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:
...
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2answers
70 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
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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 ...
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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
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2answers
56 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
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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
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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
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2answers
122 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 ...
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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 ...
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0answers
90 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
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1answer
57 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 ...
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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
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4answers
167 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 ...
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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
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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
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1answer
75 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:
...
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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
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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
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1answer
114 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
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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
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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
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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
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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 ...
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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
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1answer
126 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........... ...
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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
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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 ...
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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
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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:
...
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0answers
38 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 ...
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0answers
101 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
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1answer
37 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 ...
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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. ...
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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 ...
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0answers
59 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:
**
...
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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 ...
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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
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1answer
40 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
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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
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1answer
118 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):
...