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

learn more… | top users | synonyms

0
votes
0answers
4 views

Sequence routine (pattern) measurement

Are there any methods to measure routine in sequence. If sequence follows some routine the measurement is bigger. I guess frequency analysis and transition probabilities can be useful.
1
vote
0answers
9 views

Sequence analysis with multiple sequences

I would like to recognize different states in a sequence of multiple vectors. To make it little more clear, here is an example: I have 2 (or more) vectors in a sequence: head position(HP) and eye ...
1
vote
1answer
19 views

Length-dependent indel costs in OMA algorithm?

I re-read this article after a long time (this time paying attention to the fine print) and noticed that they use indel costs that depend on sequence length in their OMA. They argue that it is done to ...
1
vote
0answers
162 views

Using Keras LSTM RNN for variable length sequence prediction

I have a set of sequences. Each sequence is the form $\{(s_1,l_1),(s_2,l_2) \ldots\}$ where $s_i$'s are real valued numbers and $l_i$s are labels from a fixed alphabet. It is important to note that ...
0
votes
1answer
17 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
0answers
51 views

Distinguish long and short term fluctuations in time series

I have a sequence of events $(e_1,e_2,\dotsc,e_n)$, and each event $(e_i)$ is described by two features $(t_i,F1,F2)$, where $t_i$ is the time of capturing the event. The events $(e_i)$ are captured ...
0
votes
1answer
14 views

Method for inferring tree structure from messy sequence data

I have data about case events in criminal cases. These data are in the form of sequence like ...
2
votes
0answers
41 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 ...
0
votes
0answers
17 views

Mining sequential associations using entropy measures

Assume I have a sequence that looks like this: A-A-A-B-A-A-C-A-A-B-C Let's say I want to predict to use the sequences of letter that occur between one letter and ...
0
votes
0answers
53 views

RNNLIB: How to get CTC output label sequence locations?

I'm using Alex's RNNLIB (http://sourceforge.net/projects/rnnl/) with CTC output on one of my projects. I am up to the step that I have successfully trained a network with 3 hidden layers (with an ...
0
votes
0answers
28 views

Calculating the significance of lift

The lift (in data mining, especially for sequential association rules), is calculated as: "by dividing the confidence by the unconditional probability of the consequent" ...
3
votes
2answers
41 views

Position-dependent substitution cost matrix for sequence alignment

Many sequence alignment algorithms and those which measure similarity between sequences require specification of a cost matrix defined on the sequence alphabet. However, the cost incurred does not ...
0
votes
0answers
18 views

How do I calculate the inter-rater agreement for sequence alignments?

I am having this task of aligning one sequence of sentences to another sequence of sentences. Let's say we have sequence 1 and sequence 2 as an example of the task: Sequence 1:  A B C D E  F ...
0
votes
0answers
21 views

Sequential pattern mining on mutiple sequences

Can someone give me a hint about a good approach to find a frequent patterns in a multiple sequences. Each sequences is a combination of 7 characters M,E,N,S,U,R,G. The length of each sequences is ...
0
votes
0answers
15 views

Domain of sequence information

The larger project is to build an SVM model using protein sequence information as input. From the sequence [C,E,D,T....] I generate sequence based variables. For example, mass is represented by ...
4
votes
2answers
258 views

similarity measure between two different ordered sequences

I know we can quantify the similarity between two sequences with the same length and same elements by rank order correlation. But how to measure similarity between two sequences of different length, ...
1
vote
2answers
111 views

Comparing mutation frequency between a case and a pool of controls

I"m working in genomics and trying to come up with the appropriate statistical test for my question. To call mutations in a tumor's DNA, we use sequencing that samples from the total population of ...
0
votes
0answers
22 views

Help Simple Conditional Counts Example

Let's say we have a sequence $S$ \begin{align} t \quad 0 \quad 1 \quad 2 \quad 3 \quad 4 \\ S_t \quad 1 \quad 1 \quad 0 \quad 0 \quad 1 \end{align} And we want to predict $S_{t+1}$ by selecting ...
0
votes
0answers
94 views

Market Basket Analysis

I am learning "Market Basket Analysis" and I need a clarification about Advantages and Disadvantages or Pro's and Con's of the "Market Basket Analysis". And some cases where actually this "Market ...
0
votes
1answer
155 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 ...
5
votes
2answers
334 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 ...
0
votes
0answers
15 views

weighting of aligned subsequences by their length

I have a pool of subsequences, each one associated with a probability (and other properties that you don't need to know) that quantifies how frequently that subsequence occurs. In order to select ...
1
vote
3answers
82 views

Central limit theorem for sum of differences

I have a quick question. If we have a sequence of i.i.d random variables, $X_1,X_2,X_3,\ldots,X_n$. Then, we make sequence below: $$ S=X_1-X_2+X_3-X_4+\ldots+X_n $$ Does central limit theorem work in ...
3
votes
2answers
59 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 ...
2
votes
1answer
121 views

How to do centroid clustering of sequences?

I want to cluster sequences using centroids. In the hclust package it is noted that "Method "centroid" is typically meant to be used with squared Euclidean ...
1
vote
0answers
95 views

Correctness of a proof for Hodges' estimator

We know the following is Hodges' estimator: $$ \delta_n = \begin{cases} \bar{X}_n & |X_n| \geq n^{-1/4} \\ a\bar{X}_n & |X_n| < n^{-1/4} \\ \end{cases} $$ where $X_1, ..., X_n \sim ...
3
votes
2answers
211 views

Mining patterns in continuous sequence

I have data in form of $N$ sequences $s_j=(t_i, e_i)_{i\in\{1,\ldots,n_j\}}$ with $n_j$ data-points each, where $t_i$ is a time-stamp and $e_i$ is a categorial event, say $e_i\in\{A,B,C,D\}$. The $N$ ...
1
vote
1answer
231 views

Comparing two sequence objects?

Using TraMineR, is it possible to compare two sequence objects to calculate the discrepancy between them? By this I mean not comparing two sequences but two sets of ...
2
votes
2answers
42 views

Can a 1st Order Model capture information that a 2nd Order model can't?

Let's say we have some sequence $y_1 \ldots y_n$. By definition, a 2nd order Markov model can capture more information from the sequence than a first or zeroth order Markov model. What I'm interested ...
0
votes
1answer
52 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 ...
4
votes
1answer
268 views

Visualize process data

I have a dataset of order processing with 8 million rows with following columns: HistoryId - Identity column of the records ...
2
votes
1answer
93 views

Predicting on data consisting of many independent short time series?

I have a dataset which contains many (hundreds) of short (3-30 obs) timeseries of different lengths. Each series is currently represented as a number indicating how long it took to the next event. To ...
1
vote
0answers
105 views

modeling changing items in market basket analysis

I'm performing a "dynamic" market basket analysis where a customer transaction is traced from the beginning (here it has an initial basket of product) to the finalized purchase (where there is the ...
2
votes
1answer
93 views

Finding all largest sequences

What would be a good / efficient algorithm or approach to find all the largest sequences within a list of chains with varying lengths? For instance these chains: ...
5
votes
1answer
243 views

Statistical test to assess differences between two sequencing methods

To asses differences between two DNA sequencing methods (454 and MiSeq) I have made artificial mixtures of different bacteria in the lab (mock communities). An Example might be (numbers are ...
1
vote
1answer
76 views

Hypergeometric test

I have compared 1370 genes which are obtained from ChIP-sequencing analysis and 652 genes which are differentially regulated genes obtained by analyzing affymetrix 430.2.0 mouse array. When I ...
3
votes
1answer
102 views

How to measure multichannel distances between “event” sequences?

In TraMineR, seqdistmc is used to measure multichannel distances between "state" sequences. I am wondering if there is a function to measure multichannel distances between "event" sequences.
1
vote
1answer
85 views

What is the role of log2 in Elzinga's turbulence measure?

Elzinga's turbulence measure (TraMineR User's Guide, p. 85) is the log2 of the number of "distinct subsequences that can be extracted from the distinct state sequence" multiplied by "the variance of ...
36
votes
8answers
6k 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? ...
2
votes
1answer
324 views

Entropy of state distribution, complexity index and turbulence for sequences of varying length

I have a dataset of varying sequence lengths and want to calculate descriptive measured for it. The main cause of differing lengths is that some cases are right censored, and are dealt properly when ...
4
votes
2answers
440 views

Should normalization completely weed out correlation?

I have two variables: ordering & length. The former measures the ordering of a sequence (i.e. all permutations of A-B-C), and the former is the length of the sequence (i.e. A-B-C has a length of ...
3
votes
1answer
83 views

Sampling from sequence data

I work with 4 sequence datasets that I want to compare. The datasets range from roughly 150 to 2000 sequences. I've been able to use TraMineR on datasets up to 1000 sequences long, but when I try to ...
2
votes
1answer
286 views

Mean and Variance of a Set of Sequences

I am trying to find the probability distribution (like mean and variance) of a set of sequences which have different length. I came into different measurement models that quantify the distance between ...
3
votes
2answers
291 views

Comparing clustering of sequences in datasets with different N?

When doing sequence analysis using a package such as TraMineR, one can calculate a clustering based on Optimal Matching (OM) distances, and then plot it as a tree. ...
3
votes
1answer
67 views

Weightining using TraMineR

I have read some posts on weighting. However, I am still unclear on the sort of weights I need to use. I am using data from the Longitudinal Survey of Australian Youth (LSAY). This survey provides ...
3
votes
2answers
273 views

Measuring entropy for event sequences?

In TraMineR the function seqient() for calculating the entropy of a sequence object is not available for event sequences (as ...
3
votes
1answer
429 views

How to estimate the centroid of clustered sequences?

I have run a sequence analaysis using the Optimal Matching algorithm. Afterwards, I have clustered the resulting distance matrice using the Ward algorithm and calculated silhouettes as measures of ...
7
votes
1answer
377 views

When and how to use weights for sequence analysis in social science?

Weighting in sequence analysis So far, I have scarcely found papers that address the issue of weighting for sequence analysis (using for example the optimal matching algorithm). Sequence analysis ...
3
votes
1answer
207 views

Duration weighted Optimal Matching Algorithm using R

Besides the ado provided by Brendan Halpin for Stata, is there a way to pursue an Optimal Matching using the R-package TraMineR which weights OM’s elementary ...
5
votes
1answer
393 views