All Questions
Tagged with bioinformaticsjava
11 questions
2votes
1answer
172views
First order hidden Markov model with Viterbi algorithm in Java
Introduction A first order HMM (hidden Markov model) is a tuple \$(H, \Sigma, T, E, \mathbb{P})\$, where \$H = \{1, \ldots, \vert H \vert\}\$ is the set of hidden states, \$\Sigma\$ is the set of ...
- 30.2k
2votes
1answer
94views
Semi-dynamic range minimum query (RMQ) tree in Java
Introduction I have this semi-dynamic range minimum query (RMQ) tree in Java. It is called semi-dynamic due to the fact that it cannot be modified after it is constructed. However, the values ...
- 30.2k
4votes
1answer
221views
Lazy Loading a Bioinformatic SAM record
I'm currently writing an API to work with Bioinformatic SAM records. Here's an example of one: ...
- 382
11votes
5answers
2kviews
Counting relevant entries in a large bioinformatics file
I have a working example of a piece of code which opens up a file, gathers information about the contents, and outputs a map which contains the information. The file The file type is an in-house ...
- 382
5votes
1answer
3kviews
Multiple sequence alignment in Java
(The entire project lives here.) Problem definition Suppose we are given three genomic strings drawn from the alphabet of 20 amino acids: ACGH CFG EAC In ...
- 30.2k
6votes
2answers
276views
Finding the most common DNA patterns of some given length
I'm working on an algorithm to search through 100,000+ lines of dna sequencing, with the fastest time possible. Here is my current code, I was wondering if there's any ways to make this run faster: <...
- 93
2votes
1answer
63views
A Java class for reading MaCH dosage files v2.0
Version 2 of A Java class for reading MaCH dosage files ...
- 1,439
3votes
1answer
100views
A Java class for reading MaCH dosage files
A dosage file (used in computational genetics) is formatted like this: ...
- 1,439
4votes
2answers
227views
Convert impute2 files to mach format
Here is a program for converting Impute2 files into MaCH format (related to genetics). Source files include one xxx_haps file and one xxx_samples file, for example: ...
- 1,439
6votes
2answers
267views
Comparing 2 lists of peptide to spectrum rankings generated by 2 different algorithms
I'm seeking a general review, but I'm particularly interested in style. This program gets 2 lists of peptide to spectrum matches, so every spectrum title is linked to a list of 1 or 10 possible ...
2votes
3answers
3kviews
Longest DNA sequence that appears at least twice (only one DNA string as input)
My question is to find the longest DNA sub-sequence that appears at least twice. The input is only one DNA string, NOT TWO strings as other LCS programs. I have done my 4th program and it seems to be ...
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