Questions tagged [algorithms]
The algorithms tag has no usage guidance, but it has a tag wiki.
39
questions
0
votes
0
answers
13
views
Can I use Aho-Corasick for epidemic spread simulation?
I found that with this string-finding algorithm, this algo can determine if a string(person) holds something(if he has sick, already got vaccinated, and et cetera.).
I am trying to simulate an ...
0
votes
1
answer
64
views
How should I imagine the pre-indexing of suffix arrays in the STAR RNA Seq-aligner?
I'm using STAR for an internship (fusion-genes in ALL cancer) and I'd like to understand what exactly it is doing. The people at the internship don't know either how it works, given their biology ...
4
votes
1
answer
159
views
Is the algorithm of the STAR RNA Seq-Aligner similar to the Knuth-Morris-Pratt string matching algorithm?
I don't know if I'm in the right SE, if not let me know and I'll delete it.
I am reading the original publication of the STAR RNA-Sequence aligner.
Given the quoted text below I wonder if the ...
1
vote
1
answer
34
views
What is the cutoff distance in this algorithm?
In the following article:
a fast and efficient Cα-based method for accurately assigning protein secondary structure elements
What are the minimum and maximum cutoff distances in this algorithm?
Also,...
0
votes
1
answer
47
views
What does it mean by "PC" in this article?
What does it mean by "PC" in this article?
a fast and efficient Cα-based method for accurately assigning protein secondary structure elements
1
vote
1
answer
81
views
Why does randomized motif search work?
I'm looking for intuition for why a randomized motif search works. My current thinking is as follows:
We are selecting many random kmers from our DNA sequences. The chosen kmers will bias the profile ...
0
votes
0
answers
18
views
Is there a newer/better book than Genome-Scale Algorithm Design available? It's from 2015
I'm considering buying the book "Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing" by Veli Mäkinnen and others.
However, as this book was ...
1
vote
1
answer
44
views
Given two ADN sequence, can there be multiple optimal alignement? And how to optimally find them?
Given two sequences, I know we can determine optimal alignment of sequence with the Needleman–Wunsch algorithm. But is it possible that two alignments have multiple optimal alignment (I guess it would ...
3
votes
1
answer
50
views
How to optimize the number of amplicons ordered for a PCR wet experiment with several genomic ROIs?
Imagine we have an experiment for which we would like to minimize the number of purchased primers. Let's look at the layout of a single primer below:
Assume we have a precomputed set of all necessary ...
1
vote
1
answer
138
views
How to reconstruct a target string from a large set of overlapping reads
I got this question as a homework. Does anyone know how the it can be solved?
Consider a short string $r$ as a read from a string $S$ if $r$ is converted from a substring of $S$ by at most $k$ swaps ...
0
votes
1
answer
57
views
Time complexity of the Neighbors function
I implemented the following find_neighbors_with_expected_hamming_distance function that generates all k-mers of Hamming distance at most d from the given Pattern.
...
2
votes
0
answers
44
views
Explaining the algorithm of RNA folding: what each symbol & value represents?
I need someone to explain to me from the nuts and bolts how algorithms/ maths is used to work out RNA folding. Explain it to me like I am an alien or child.
I am looking at this paper - https://eprint....
0
votes
1
answer
102
views
Why use Needleman-Wunsch if there is no way to evaluate the statistical significance
I thought that Needleman-Wunsch is the best approach to align sequences. However, I read that it is impossible to evaluate the statistical significance of the alignment if you do global alignment. So ...
1
vote
1
answer
73
views
Evaluating amateur bioinformatics results
I've might have created a new algorithm for finding patterns in DNA. The technique has not been used before, and it managed to find a 33-mer with corresponding complement that exists both in E. Coli ...
1
vote
0
answers
38
views
Kinetics "Master Equation"
In stochastic (probabilistic) models, the evolution of a system over time is calculated using a "Master Equation" which also factors the external and internal noise / perturbations in order ...
3
votes
2
answers
391
views
mapping heteryzygous kmers on a genome
I have a set (a couple of millions) of kmer pairs of known length (usually 21) that I know that are heterozygous in the middle nucleotide. For instance:
...
4
votes
1
answer
90
views
Attractor Landscape Analysis
I have come across a modeling toolbox, ATLANTIS, which is able to determine cell fates in silico based on the input models provided. This MATLAB-based toolbox is built on a method called "Attractor ...
1
vote
3
answers
59
views
How to score how densely bases are distributed along a given oligo?
Suppose I have a short chain string of oligos, and I want to rate them from 0 to 1 based on how clustered the "A"s are in respect to the chain. For example:
...
4
votes
1
answer
151
views
Prediction of prokaryotic origins of replication (ORI)
I want to predict origins of replication (ORI) on hundreds of prokaryotic genomes. The most straight-forward solution would be to use most commonly used tool, Ori-Finder.
It uses integrated gene ...
1
vote
1
answer
105
views
Non-random access on a fastq file
There was a nice question on random access on a fastq file, however I have the opposite problem. I want to programatically access non-random fastq entries quickly (using C++).
Say I have several ...
2
votes
1
answer
155
views
How is consensus alignment for OLC assembly usually implemented?
Background
In C++ I want to implement a simple class that performs overlap layout consensus assembly but I can not figure out the most logical data structure to use for the consensus alignment step.
...
1
vote
1
answer
71
views
How do I interpret the function O(f^-2 log n) in Shekhar et al. (2017)?
The results of Shekhar et al. (2017) "indicate that ASTRAL requires
$\mathcal{O}(f^{-2} \log{n})$
gene trees to reconstruct the species tree correctly with ...
0
votes
1
answer
57
views
What are some of the major questions pursued by the field bioinformatics? [closed]
I am an occasional user of tools in bioinformatics and I am fascinated by the possibility of uncovering deeper patterns in the biological realm using the help of computer algorithms. Yet I don't know ...
3
votes
1
answer
163
views
Histosketch vs Count-Min sketch: preserving similarity
A preprint describing a new tool and its application to microbiome analysis was recently published in bioRxiv[1]. At the core of this new tool, HULK, is a new data structure called a histosketch[2] ...
6
votes
1
answer
117
views
Getting all NNI trees of a parsimony tree
I have an aligned protein sequence file which I have been using for reconstructing a parsimonious tree. I am currently using NNITreeSearcher._get_neighbors method from Biopython 1.72 but it's way to ...
4
votes
1
answer
310
views
Efficiently aligning a lot of reads on the same small reference sequence
The context: I have a DNA-sequence coding for a protein, about 1500 bp in length. Using NGS, a lot of reads of (mutants of) this same sequence were acquired. All of these reads need to be aligned to ...
1
vote
0
answers
28
views
Stand alone chaining tool for existing blast hits?
I have a table of blast hits in a database that I'd like to chain. What is a good choice for a 'stand alone' chaining tool? Is it simple to implement in Perl, for example?
Example 'hit' data is here. ...
4
votes
2
answers
87
views
Do any computational phylogenetic methods enable the specification of ancestral states?
Various phylogenetic algorithms estimate ancestral states of a phylogenetic dataset. Is there a way in either maximum parsimony, distance-based methods, or Bayesian inference to indicate what the ...
0
votes
2
answers
85
views
Why does `pratchet()` in `phangorn` not find the most parsimonious trees?
I called pratchet() on a dataset with binary values for the characters and it returned a parsimony value of 35. I then calculated the parsimony value for the ...
7
votes
2
answers
508
views
How does htslib/samtools access optional BAM fields?
I am confused regarding how various software libraries deal with optional fields in a BAM:
Based upon the BAM specification, there are 11 mandatory fields to a BAM:
...
8
votes
3
answers
414
views
Books on bioinformatics algorithms
I'm looking for a book about bioinformatics algorithms, such as alignment, BLAST search, and variant calling.
I'm hoping reading about this subject will give me a deeper understanding of the ...
4
votes
2
answers
103
views
How does Li and Durbin's BWA paper compare alignment programs on real data?
Li and Durbin's "Fast and accurate short read alignment with burrows-whleeler transform" found here, says:
We evaluate the performance of BWA on ... real paired-end data by
checking the fraction ...
2
votes
1
answer
259
views
How is a principal component analysis for population structure made from a bam or other alignment file?
I'm curious how a PCA for population structure is built from an alignment/BAM or SAM file. How do programs like angsd and ngsCovar actually build a PCA? What exactly makes things come out as different ...
6
votes
2
answers
263
views
Estimate the length of poly-A tails from randomly-primed RNAseq data
So a poly-A tail is a long chain of adenine nucleotides that is added to a messenger RNA (mRNA) molecule during RNA processing to increase the stability of the molecule.
For my project, I would like ...
3
votes
0
answers
42
views
Large range parameter identification
I have a model (ODE) of an enzymatic reaction, and I'd like to estimate four of its parameters to fit some available data. To obtain the model I am just using Mass-Action Kinetics.
Some more details:
...
1
vote
2
answers
164
views
Can structural - equation modeling be used in Bioinformatics?
I am a bioinformatics student and I was learning the basics of structural equation modeling (SEM).
I was wondering, are there any applications of SEM on bioinformatics? Are there any strong sides ...
5
votes
0
answers
72
views
Help with identifying disease modules [closed]
I've made an application that at this point ranks all combinations of drug pairs relevant to a biological network/graph in the order of how disruptive the outcome of deleting the targets of a given ...
8
votes
1
answer
5k
views
How are MACS2's narrow peak and broad peak algorithms different?
The peak calling tool MACS2 can call peaks in either narrow peak mode (for focused signals like transcription factor ChIPseq) or broad peak mode (for more defuse signals, like certain histone ...
23
votes
4
answers
2k
views
Are there any rolling hash functions that can hash a DNA sequence and its reverse complement to the same value?
A common bioinformatics task is to decompose a DNA sequence into its constituent k-mers and compute a hash value for each k-mer. Rolling hash functions are an appealing solution for this task, since ...