Questions tagged [dna]
The dna tag has no usage guidance.
40
questions
6
votes
2answers
350 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
12 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 ...
2
votes
1answer
106 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
57 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
70 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
41 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
290 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
53 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 ...
4
votes
1answer
676 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
46 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
78 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
160 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
83 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
279 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
302 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
577 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
237 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
68 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
79 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
91 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
26 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
2answers
99 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 ...
3
votes
1answer
783 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
146 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
52 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....
1
vote
2answers
475 views
Why do NEB adapters have non-complementary sequence?
I am making some infographics of different library prep types and noticed something weird about NEB's Ultra II adapters.
Molecule 1 is the desired product of the ...
13
votes
7answers
4k views
What is the fastest way to get the reverse complement of a DNA sequence in python?
I am writing a python script that requires a reverse complement function to be called on DNA strings of length 1 through around length 30. Line profiling programs indicate that my functions spend a ...
2
votes
1answer
81 views
How to retrieve SNPs data of different humans?
How can I retrieve only SNPs from the dbSNP's FTP site. The files are gzipped and organized by human chromosome (i.e, chr[1-22,X,Y]), are these for one human? I need only SNPs data for various humans.
3
votes
1answer
51 views
predict the foldability of single-stranded DNA molecules
I have a list of regions of the human genome and I want to predict if single-stranded molecules in a buffer would tend to fold and create pin structures by sequence self-complementarity. What's the ...
2
votes
1answer
143 views
How can I calculate the silent mutation for each position in codon?
I am trying to find the number of silent mutations in for each position in codon.
In the homework, I am asked:
For the codons and for each position, count the number of silent mutation. There are ...
5
votes
2answers
1k views
Way to get genomic sequences at given coordinates without downloading fasta files of whole chromosomes/genomes first?
So I have a list of start and stop positions along chromosomes in different species, and I'd like to get the corresponding DNA sequence for each set of coordinates. In the past, I've just download the ...
4
votes
1answer
198 views
Software recommendations - DNA composition
I'm looking to generate data based on the DNA composition of a region of my genomes (data is incomplete genomes from HiSeq runs in fasta format). I'm looking for software which will give me sliding ...
24
votes
4answers
4k views
Why sequence the human genome at 30x coverage?
A bit of a historical question on a number, 30 times coverage, that's become so familiar in the field: why do we sequence the human genome at 30x coverage?
My question has two parts:
Who came up ...
12
votes
2answers
182 views
Is there a standard k-mer count file format?
I am doing a research project involving calculating k-mer frequencies and I am wondering if there is any standard file format for storing k-mer counts.
4
votes
2answers
1k views
how is the DNA Integrity Number (DIN) calculated in Bioanalyzer/TapeStation?
For DNA/RNA quantification machines like the Bioanalyzer or TapeStation, the DNA Integrity Number (DIN) or RNA Integrity Number (RIN) numbers are quoted as a measure of the fragmentation of the ...
3
votes
0answers
752 views
How to install DnaSP on a Mac
I need to install DnaSp,
but its not working on my mac. I'm using wine to install it using these instructions for wine.
it successfully installs but then I get this error
...
0
votes
2answers
96 views
How can I find the relevant pathway map from gene-gene or protein-protein interaction list? [closed]
I have some difficulties to understand/interpret the pathway map and how a gene-gene interaction list or DNA sequencing can map into pathways.
In addition what's the difference between MARK/ERK ...
6
votes
1answer
80 views
State of the art in predicting Translation Initiation Sites
I'm working on a university project of predicting Translation Initiation Sites in human DNA. I searched the net for papers and documentation to get guidelines and inspiration, but I feel uncertain ...
11
votes
5answers
284 views
Improve a reference genome with sequencing data
I have a DNA sample which I know doesn't quite match my reference genome - my culture comes from a subpopulation which has undergone significant mutation since the reference was created.
From visual ...
17
votes
2answers
410 views
Accuracy of the original human DNA datasets sequenced by Human Genome Project?
The Human Genome Project was the project of 'determining the sequence of nucleotide base pairs that make up human DNA, and of identifying and mapping all of the genes of the human genome'. It was ...
