Questions tagged [sequence-analysis]

Analysis of a DNA, RNA, or peptide sequence to understand its features, function, structure, or evolution.

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544 views

How to calculate a blosum matrix with X% identity?

Calculating a blosum matrix is easy and many explanations online exist. However, given a set of sequences and asked to get X% identity I am unsure of. Say they said 80% identity with the following ...
0 votes
1 answer
48 views

Optimization of fault diagnosis sequence using probability and cost [closed]

I am developping the algorithm to optimize the fault diagnosis sequence using probability and cost. For exemple, I have 3 diagnosis actions possibles : option 1 : probability which can detect the root ...
0 votes
0 answers
22 views

Random sequence generator algorithm non informative piror distribution

I want to conduct a Bayesian statistical analysis of a sequence generation phenomenon. The sequences generated contain elements from a known alphabet. Working on that, I have tried to define the prior ...
1 vote
1 answer
510 views

Handling missing data in Sequence Analysis (TraMineR) within the observation window

I´m using sequence analysis. I have a question about how to deal with missing data within the observation window. The starting point of the analysis is when respondents leave secondary school (t0). I ...
0 votes
1 answer
41 views

How to look at between-group differences for a single gene using RNA seq data

I have an RNA seq dataset, but I am only interested in the expression of a single pre-specified gene and to compare it between 2 groups (patient phenotypes). Some have suggested (without a reference) ...
0 votes
0 answers
8 views

How to set values for Needleman-Wunsch algorithm so raster shifts are not penalised?

I recently found out, that the Needleman-Wunsch algorithm (NW) comes very close to what I need to match my patterns. In particular, I have 2 sequences (toy example): ...
0 votes
0 answers
10 views

LMEM for low number of data points?

I have DNA and RNA counts of 4 time points with 4 replicates. I want to quantitate the change in RNA copy number relative to DNA copy number for each gene in the genome. I especially interested to ...
0 votes
1 answer
99 views

Why use sliding window input features in sequence modeling?

I was reading through the DNABERT paper and found that their input features were k-mers. This is equivalent to using rolling/sliding window features in the other common family of sequential problem, ...
0 votes
0 answers
680 views

What does it mean if a simple linear neural network performs better than an LSTM on sequential data?

I'm working on a genetic data project, where one data sample is represented as sequences of integers (of length 2000) and it needs to be classified into one of 4 classes, so I guess it is similar to ...
1 vote
1 answer
43 views

Statistical significance in known population

I am working with a data set with the sequence identity (a value in [0,1] representing the conservation between sequences) of many genes for many bacterial strains. I would like to be able to draw ...
2 votes
1 answer
90 views

Sequence prediction: ambiguity in training set

There is a set of sequences (train set), where each element is one or multiple tags: A, B -- A -- Z -- Z, A B -- A -- Z -- D ... Given a new sequence: ...
4 votes
2 answers
2k views

Clustering customers by their orders sequence patterns

I have dataset with clients orders. Example: ...
2 votes
1 answer
515 views

Sequences comparison metrics

I know about Edit distance, Longest Common Subsequence and their normalized versions to measure the similarity between sequences But do we have any similarity measures other than the above ones?
1 vote
1 answer
61 views

How to test differences (over time and between treatments) of a specific species in DNA metabarcoding sequencing data?

I have DNA metabarcoding sequencing data in the following format: plot Time_point reads_species_A Reads_species_B reads_species_C 1 T1 0 245 65 2 T1 48 455 0 3 T1 15 5 10 1 T3 153 23 564 2 T3 ...
1 vote
2 answers
290 views

Weird Cooks distance results using DESeq2

I'm currently trying to assess fold change when comparing two different sample types using DESeq2 package and I'm getting weird Cook's distance values which are causing major problems. The two ...
20 votes
5 answers
5k views

Framing the negative binomial distribution for DNA sequencing

The negative binomial distribution has become a popular model for count data (specifically the expected number of sequencing reads within a given region of the genome from a given experiment) in ...
1 vote
1 answer
129 views

Multichannel distance from a reference sequence

I am working with a large dataset and applying multichannel sequence analysis to two life course domains. I would like to adapt a solution suggested in the post below to multichannel sequences, but I ...
0 votes
0 answers
44 views

Statistical similarity on sequences

What are the methods that can be used for evaluating the similarity of the sequences? Lets say that we have three sequences; I want to be able to say that "statistically" the sequence number 1 and the ...
0 votes
1 answer
963 views

A method for clustering 1D signals?

I have samples from 150 different genes containing the following information: sequence of the gene signal strength along the length of the gene (the signal can be negative or positive). I have ...
117 votes
17 answers
53k views

What is the role of the logarithm in Shannon's entropy?

Shannon's entropy is the negative of the sum of the probabilities of each outcome multiplied by the logarithm of probabilities for each outcome. What purpose does the logarithm serve in this equation? ...
0 votes
0 answers
366 views

Training and testing transformer model from scratch

As you know, transformers are one of the strongest model in the field of NLP and machine translation. I know there are many resources, but I still could not find a good tutorial teaching how to use ...
9 votes
4 answers
3k views

Sequential pattern mining on single sequence

Can someone give me a hint about a good approach to find a frequent patterns in a single sequence. For example there is the single sequence ...
2 votes
0 answers
394 views

How to calculate the evaluation metrics on streaming data for online ML algorithms

I am working on a binary classification problem where I need to develop an online ML model that can work on streaming data. However, I am not sure how can I use the evaluation metrics for ...
4 votes
2 answers
259 views

How to interpret p-values in output of seqecmpgroup()?

The seqecmpgroup() function returns a table that, among other things, include p-values for each identified subsequence. How should these be interpreted? I can see ...
1 vote
1 answer
112 views

Viewing automated cost matrix for DHD in TraMineR

I'm using social sequence analysis, and comparing between different distance methods for my data. I'm wondering if there is a way to view/call the automatic substitution cost matrix that the dynamic ...
0 votes
1 answer
29 views

Determining a p-value for a test statistic that depends on other test statistics

Sorry for the confusing wording of the title. If some has any better way to word it, please feel free to change it. Background For those unfamiliar with bioinformatics data, I have data from a ...
5 votes
0 answers
323 views

Detecting statistically significant clustering of continuous values

I'm working with biological sequence data where each position in the sequence has an associated continuous value. I'm ignoring the sequence content so the data is very similar to a time series with ...
1 vote
1 answer
43 views

Why shouldn't you mix variable size inputs in the same minibatch?

I am trying to build a CNN-LSTM architecure in tf.keras that classifies sequences of varying sizes. My training data is highly variable and I would have to crop/pad sequences in order to create ...
2 votes
0 answers
432 views

Building RNNs on mixed sequential and non-sequential data

I have a data set that is a bunch of windows, for each window I want to perform regression. The windows themselves have four sequential features that span back about 24 time steps. Additionally each ...
0 votes
0 answers
20 views

Choosing a model for input: categorised, weighted sequence, output: binary variable

What would be an appropriate model for predicting a binary target variable, given a weighted sequence? Sequences will be reasonably short, typically between ~ 1 and 5 elements. I have in the order of ...
2 votes
2 answers
8k views

Sequence classification via Neural Networks

What exact kind of architecture of neural networks do I need for a sequence binary/multiclass classification? The sequences can be of different length and are to be discriminated by a certain ...
2 votes
2 answers
885 views

Sequence prediction based on non-sequential inputs

I have a dataset with timestamps and event values (true or false -- these are based on sensor data which detect room occupancy). I'd like to build a model that would take a timestamp as an input and ...
1 vote
0 answers
29 views

What are the classifiers that can be used for sequence data?

I've been going through the classifiers like Naive Bayes, Decision Tree etc. I've a sequence data like so ...
4 votes
1 answer
415 views

Unsupervised clustering of sequence of events to subsequences

I have a big dataset of M sequences of [1 - N] events, where each event has multiple properties (start date, end date, location, ...
0 votes
1 answer
167 views

Binary Sequence Prediction Model with Time dependant features

I got a very long sequence of binary items (0 or 1). Each item is associated to a timestamp. For example : ...
0 votes
0 answers
24 views

Predicting the Winner of a sequence of numbers

I have various series of numbers of different lengths (ranging from 4 to 10) such as the example below: [1.5, 5.0, 6.0, 6.0, 8.0] [1.4, 6.0, 7.5, 9.0, 50.0, 100.0, 200.0] For each one of them I ...
1 vote
0 answers
80 views

Analyse set of Sequences of varying length with PCA?

Task description I have a dataset with strings indicating the sequence of the screens a user visit when making a purchase on an app. A string could be: "1,2,1,2,3,3,4,5,6,7,3,2,5,6". Another string ...
1 vote
0 answers
96 views

Likelihood Matrix from a Random Forest?

I'm going through the supporting material of a paper (https://science.sciencemag.org/content/360/6384/81) , trying to reproduce their results (see below, note that HVG=highly variable gene). The data ...
1 vote
0 answers
39 views

Ideas for determining the optimal sequence of calls and emails to maximize the probability of a sales lead converting to a sale?

I have a large data set of sales leads that are in the form of a lead_id, a sequence of binary integers that denote the order of emails and phone calls made to a sales lead, and the binary outcome of ...
1 vote
1 answer
89 views

have many error likelihoods, how to combine to get a confidence or p value?

I'm working in bioinformatics and its been a long time since I dusted on my statistics. Basically I'm working on variant calling which amounts to sequencing a large number of sequence reads and ...
8 votes
2 answers
397 views

Identifying sequential patterns

I am working with sequence data which are long lists of malware win-api calls. I am trying to cast the problem of identifying 'malware behavior' into one of finding sequential patterns. I treat each ...
3 votes
0 answers
295 views

Which distance metric to use to cluster categorical sequences (clickstreams or clickpaths)?

For my research, I want to cluster website visitors based on their clickstreams to understand different information behavior patterns (i.e., customer/visitor journeys). The data can be characterized ...
0 votes
1 answer
50 views

ATGC sequence of gene expression data [closed]

I am not a pro in genetics so please excuse my non-technical language. I need dataset which contains the gene expression as well as the associated ATGC sequence with each gene expression value. For ...
7 votes
0 answers
783 views

traditional state-space models and LSTMs

I am trying to understand the nature of LSTMs in relation to intuitions from traditional state-space models (e.g., Kalman filtering). The code below aims to simulate a simple univariate linear state-...
3 votes
2 answers
112 views

Localized distance function on sequential binary data

I am trying to find a good distance function for sequential data that is all binary. For now, I am using Edit distance however I have some more domain-specific knowledge that I would like to ...
1 vote
1 answer
468 views

Determining the class of a new sequence using Markov chains

I want to use a Markov chain to classify a new given sequence as from model+ or model-. For that purpose first I trained two ...
3 votes
1 answer
4k views

what is "target delay" in the context of RNN/LSTM?

I'm currently reading a paper on sequence-to-sequence classification (speech-to-text) and it is stated that "there are ways to introduce future context, such as adding a delay between the ...
0 votes
1 answer
99 views

Is using "Normal Approximation to binomial distribution" to test mutation enrichment in genomic region correct?

We are analyzing cancer patient mutation data. We defined set of region on the human genome as binding events, (for the ones who is interested in to the subject, it is a transcription factor binding ...
2 votes
1 answer
132 views

Calculating p-values for ratios of binomial variables

I have a problem that I will express in 2 ways: a math-y way and a biology way. Hopefully this will make it more clear. Math-y way: I have N observations of a pair of binomial variables, call them ...
5 votes
1 answer
4k views

Analyzing Sankey diagrams statistically?

Sankey diagrams are helpful for visualizing multiple, interacting processes: Are there any statistical tools available that can analyze the interactions of multiple processes? I'm aware of sequence ...