Questions tagged [dna]
Acronym for deoxyribonucleic acid, the unit of inheritance for all eukaryotic and prokaryotic organisms
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questions
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1answer
25 views
What are the applications of DNA or RNA pattern matching?
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
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0answers
28 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
36 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:
...
2
votes
2answers
37 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
42 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
49 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
35 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 ...
5
votes
1answer
105 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
16 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
36 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
279 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
10 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
92 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
56 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
48 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
12 views
Swapping to effect increasing allele in case/control studies
I want to find the effect-increasing allele for a given set of SNPs. For quantitive traits, I understand the effect sign is changed when the A1 and A2 are swapped. How does this work for odds ratios?
...
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0answers
34 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
26 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
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0answers
34 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 ...
1
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0answers
48 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
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
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0answers
23 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 ...
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0answers
32 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
19 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 ...
2
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0answers
49 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
18 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
39 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
25 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
37 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
84 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
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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
76 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 ...
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0answers
34 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
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1answer
39 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
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0answers
47 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
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0answers
44 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 ...
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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 (...
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8answers
5k 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
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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
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1answer
49 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 ...
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0answers
18 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 (...
5
votes
3answers
579 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 ...
8
votes
2answers
623 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 ...
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0answers
19 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
I'm a little bit confused on how to interpret the result.
is there a way to get the ...
3
votes
1answer
352 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
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1answer
70 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
110 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 ...
1
vote
1answer
44 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 ...
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3answers
713 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 ...
