Questions tagged [dna]

Acronym for deoxyribonucleic acid, the unit of inheritance for all eukaryotic and prokaryotic organisms

Filter by
Sorted by
Tagged with
0
votes
0answers
24 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
21 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
33 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
20 views

How to compare 2 AGTC sequences of homo sapiens and pan troglodytes?

I'm the beginner and I want to compare DNA of Homo sapiens and Pan troglodytes. I have taken files from here and downloaded homo sapiens primary assemmly file and pan troglodytes toplevel file, but ...
0
votes
0answers
26 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
17 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
vote
0answers
45 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
vote
0answers
15 views

mining DNA barcodes from Genebank/BOLD per location

Is there a method to download all the sequences for a particular DNA barcode region (e.g; ITS2, rbcL or trnL) only for species within a particular distribution (e.g. Panama). Hopefully, the specimen ...
1
vote
0answers
36 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
22 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
26 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
31 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
60 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
50 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
33 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 ...
1
vote
1answer
36 views

Why do we scale the rate matrix of a substitution model to make the average rate of substitution equal 1?

The matrix of transition probabilities for a substitution model Q over time t is found as follows: $e^{Qt}$. Since Q and t only show up as a product, we cannot distinguish time and rate of change. So ...
3
votes
0answers
46 views

Theoretical limit of human genome compression

How small can a compressed file containing the human genome be? I'm aware that this question cannot actually be answered, since it is asking for the Kolmogorov complexity of the human genome, which ...
0
votes
0answers
39 views

Compressing the human genome to few megabytes

Multiple sources (see for instance this or this) discuss how genetic data will have scalability problems, given the huge file size of the human genome. The most straightforward encoding (see here) of ...
0
votes
0answers
24 views

Coding object structure properties into a sequence

Hopefully, I found the right place to ask. Please, note that I'm not a specialist in the current field. Is there an algorithm to code information about object structural properties into a sequence (...
2
votes
1answer
294 views

Are the conclusions in “The proximal origin of SARS-CoV-2” legit?

I don't have any background in genetics and bioinformatics, so I ask you if you think that the arguments provided in the article The proximal origin of SARS-CoV-2 by Andersen et al. are convincing. In ...
19
votes
8answers
4k views

Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done? [closed]

I'm confused about the difference between genome and DNA. Is it correct to say that the same type of bacteria has the same DNA? But my understanding is that it is not correct to say that the same type ...
0
votes
0answers
24 views

What are the meanings of these transcript ids?

I have three types of transcripts for Rosa chinensis "Old Blush" homozygous genome v2.0 from GDR genome browser. ...
1
vote
1answer
38 views

How to calculate Centimorgan lengths from run lengths in one-to-one dna profile comparison

For easier management of a database of dna profiles, I'm creating a tool to perform one-to-one matching on two profiles with snp genotype information. Basically, something that works similar to ...
1
vote
0answers
17 views

How can I find genes of fundamental metabolic processes for an organism?

I want to find genes of fundamental metabolic processes in the Phytophthora cinnamomi genome. I'm using the genome sequence deposited in the NCBI and I'm searching ORF by ORF, using the ORF finder (...
3
votes
2answers
189 views

How to translate amino acid sequences to Nucleotide sequences

I want to convert a list of fasta ( protein sequences) in a .text file into corresponding nucleotide sequences. A Google search gives me result of DNA to protein conversion but not vice versa. Also, I ...
6
votes
2answers
435 views

What is 'k' in sequencing?

When a DNA sequence is sequenced, I've only ever dealt with A,T,C,G and N which indicates un-identifiable bases. However, I came across a 'k' recently and I had asked another researcher who gave me an ...
1
vote
0answers
14 views

How can I get the estimate of lmFit function form limma package

This is the first time that I used lmfit function from the limma package and I'm a little bit confused on how to interpret the result. Also, is there a way to get ...
3
votes
1answer
208 views

What are Orthogonal DNA Sequences?

When reading a paper, I came across the following statement Standard vectors were constructed, flanked by pairs of homology sequences derived from yeast barcodes at the ends of each expression ...
1
vote
1answer
65 views

How many types of DNA methylation are there?

My current understanding is: bases A or C can become methylated due to interaction with a methyltransferase these methylations ...
3
votes
2answers
88 views

Produce a single sequential FASTA sequence out of BAM

I'm having problems properly looking for a solution because I'm a layman in Bioinformatics not familiar with the terminology. I'm hoping you can nudge me in the right direction, please! Thank you very ...
0
votes
1answer
42 views

Function to find ATP binding sites

I'm currently doing a python project where I need to write code that extracts the ATP binding site from a FASTA file using a regular expression. I've tried the following code but it does not work. It ...
1
vote
3answers
493 views

Calculate the occurrence of motif in sequences (including overlaps) using Python

I need to calculate the occurrences of a motif (including overlaps) in sequences (motif is passed in the first line of standard input and FASTA sequences in subsequent lines). The sequence name starts ...
2
votes
1answer
59 views

Alignment for predicting DNA hybridization?

I am currently working on a Computer Science project where we are trying to build a large set of orthogonal single-stranded DNA sequences. The goal would be to ensure that when put in solution, the ...
5
votes
2answers
1k views

What is a quick way to find the reverse complement in bash

I have a DNA sequence of which I would like to quickly find the reverse complement. Is there a quick way of doing this on the bash command line using only GNU tools?
2
votes
1answer
49 views

Restriction enzymes with multiple recognition sequences

In a bioinformatics programming course I am currently teaching (using Python, and approached from a mostly CS rather than a biology background) I assigned a project which involves finding sites where ...
3
votes
1answer
83 views

programmatic secondary structure prediction for >36-mer DNA oligonucleotides

I'm writing a tool to automate Sanger sequencing primer design for a production lab that uses a universal-tail chemistry Sanger sequencing to verify NGS results. Essentially, the template DNA is ...
1
vote
0answers
232 views

Aligning nucleotide sequences in APE software

I am very new to APE software. I am trying to align complementary oligo-DNA strands using APE on macOS. I have both the forward and reverse sequence of an oligo-DNA insert in two separate files. But I ...
6
votes
1answer
210 views

What is Allelic Imbalance

Can anyone help me explain what allelic imbalance is, hopefully shortly? Surprisingly, we cannot find any introduction online.
4
votes
1answer
562 views

What are 2D reads in the Oxford MinIon?

Reading the Mash: fast genome and metagenome distance estimation paper, I see the reference to "2d reads" notion under the minION context (a sequencing technique) e.g ...
1
vote
1answer
521 views

What i5 index should I use on the Illumina sample sheet for an unindexed p5 primer?

I have an upcoming run on a HiSeq X and most of the libraries in the pool have both i5 and i7 indices. However, some of the libraries were made with the IS4 p5 oligo and it is unindexed. The IS4 ...
2
votes
0answers
762 views

Searching for start and stop codons for protein sequencing of contigs

I need to convert contigs into their respective protein sequences given a reference genome (i.e. I need to take a substring, whose position is already known on the string, and I need to locate the ...
4
votes
1answer
298 views

How to map short sequences to long reads, recovering all multiply-mapped high-quality matches

The dilemma: I have a problem where I have around one million short sequences (21 bp to several 100s of basepairs) for which I need to identify all occurrences of in 20-30x coverage noisy long reads (...
3
votes
1answer
79 views

Do people today with a disease caused by single gene mutation that is inheritable - all share a common ancestor?

First question here so sorry if it is about both genetics and evolution. So, if I get a disease which can be clearly identified on the gene level and all my descendants inherit it, after 500 years do ...
2
votes
2answers
90 views

How to map reads shorter than 32bp with minimap2?

I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: ...
2
votes
1answer
104 views

Minimap2 -ax map-pb doesn't output tlen field

I have used minimap2 to map some pacbio reads to a reference genome. I would like to know the "insert size" (true length of sequence) relative to the reference. More specifically, I want to know the ...
2
votes
0answers
27 views

Alignment using secondary and tertiary features of DNA

I m trying to align different sequences of length not greater than 50. Is there any way to incorporate other information such as stacking energy, entropy, bonds etc. If there any way to align ...
3
votes
3answers
117 views

Effect of mutation in DNA sequence on transcription factor binding sites

How much does a single mutation/alteration of a nucleotide affect the presence of a transcription factor binding site (TFBS)? I am from computer science background(Obviously). I want to make a ...
4
votes
1answer
1k views

Why do NEBNext indexing primers have sequence between the p5 oligo and index?

In a previous post I asked Why do NEB adapters have non-complementary sequence? Since then, I realized that there is some other sequence in the p5 indexing primer, as well as in the p7 indexing ...
0
votes
1answer
197 views

single stranded cDNA vs double-stranded cDNA

Single stranded cDNA is used by race pcr and rt-pcr while next-gen sequencing (Illumina) requires double stranded cDNA. What is the reason behind this ?
0
votes
1answer
68 views

Help Adjusting Bedtools Output in R

I have been asked to write a script in R to edit, using data.frame, this .fa file that is the result from extracting gene sequences from a repeat masker coordinate file on the genome I am working with....