Questions tagged [bioinformatics]

Bioinformatics is the use of software tools to analyse biological data.

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1answer
47 views

A Java class for reading MaCH dosage files v2.0

Version 2 of A Java class for reading MaCH dosage files ...
3
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1answer
86 views

A Java class for reading MaCH dosage files

A dosage file (used in computational genetics) is formatted like this: ...
4
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2answers
212 views

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: ...
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0answers
92 views

Finding the Cox regression coefficients in a mixed model for microarray data

I have written a code for a project which aims at finding the Cox regression coefficients in a mixed model for microarray data. The study was carried out on the Affymetrix Hgu133a platform. In the ...
2
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1answer
309 views

Slow Python text-processing script

This script of mine merges columns 1 and 2 from one input file and sees if these merged combinations exist in the other infile (and vice versa). I know I get stuck in appending. It did not get past ...
4
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0answers
155 views

Vectorize Fisher's Exact Test

I have two data frames/ lists of data, humanSplit and ratSplit, and they are of the form ...
1
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1answer
769 views

Faster way to parse file to array, compare to array in second file, write final file

I currently have an MGF file containing MS2 spectral data (QE_2706_229_sequest_high_conf.mgf). The file template is here, as well as a snippet of example: ...
8
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1answer
5k views

Genetic Algorithm in Python

I'm a new programmer, so any help is welcome. Preferably to make it faster, avoid heavy memory usage, and so on. ...
6
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2answers
259 views

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 ...
11
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3answers
3k views

Counting DNA nucleotides in C

I have written code to solve the following Rosalind problem. This is my first time writing in C and I would like a review of my code, particularly in regard to correctness and performance. ...
3
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1answer
916 views

Calculating overlap of segments in chromosome data

I wrote an R code that basically performs 2 operations: For each segment in file A, find all segments in file B that lie in that segment. Find the percentage of overlap for each case in previous ...
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2answers
1k views

Parsing BLAST output in XML format using Regular Expression

There many other better ways to parse BLAST output in .xml format, but I was curious to try using regex, even if it is not so straightforward and common. Here is the code how to extract translated ...
3
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2answers
680 views

Rosalind's 3rd problem in Scheme

I have an imperative programming background and I've decided to study functional programming by applying it to problems found on sites such as Project Euler and Rosalind. My language of choice is ...
4
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2answers
165 views

Data screening using Perl

Background information I've been asked to write a little Perl script that allows genomic data to be screened against reference files in order to determine locations of specific mutations. The input ...
6
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2answers
110 views

Foreach-loop for and print commands

How can I make the following code shorter or efficient (maybe with other loops or other nice ideas), and keep the current functionality? ...
6
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2answers
1k views

Genomic Range Query

Recently I worked on one of the Codility Training - Genomic Range Query (please refer to one of the evaluation report for the detail of this training). The proper approach for this question is using ...
11
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2answers
8k views

Calculating the joint probability of n events from a sample sequence of occurrences

I'm writing an algorithm to take in a sample list of sequences of events, calculate 1-step transitional probabilities from the sequences, forward or in reverse, then calculate the joint probability of ...
5
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1answer
121 views

Case study with a biological populations: a list of lists of lists

I have a population (Pop) which has an attribute which is a list of individuals (Ind) where each individual has an attribute ...
4
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2answers
2k views

How to improve this Needleman-Wunsch implementation in C#?

I split my implementation of this sequence alignment algorithm in three methods. Where NeedlemanWunsch-method makes use of the ScoringFunction and the Traceback methods. Further I decided to go with ...
6
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3answers
2k views

Optimization for SQLite result set parsing

I am retrieving information from an SQLite database that gives me back around 20 million rows that I need to process. This information is then transformed into a dict of lists which I need to use. I ...
4
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1answer
231 views

Cutting strings into smaller ones based on specific criteria

I've got this largish (for me) script, and I want to see if anybody could tell me if there are any ways to improve it, both in terms of speed, amount of code and the quality of the code. I still ...
6
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1answer
3k views

Calculate query coverage from BLAST output

I have a BLAST output file and want to calculate query coverage, appending the query lengths as an additional column to the output. Let's say I have 2 7 15 <...
7
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4answers
7k views

Genome string clump finding problem

I am trying to solve a bioinformatics problems from a Stepic course. The problem posed: find clumps of the same pattern within a longer genome. Motivation: Identifying 3 occurrences of the same ...
2
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3answers
2k views

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 ...
5
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1answer
673 views

SAM mapped reads

I write quite a bit of code in C, but haven't done much C++ since my college CS classes. I have been revisiting C++ recently, and thought I would re-implement a program I had previously written in C, ...
5
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2answers
3k views

Efficient parsing of FASTQ

FASTQ is a notoriously bad format. This is because it uses the same @ character for the id line as it does for quality scores. Deciding what is a quality score and ...
8
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3answers
564 views

Statistical calculations with sets of genes

The following piece of code executes 20 million times each time the program is called, so I need a way to make this code as optimized as possible. ...
5
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3answers
795 views

FASTA file processing using Python to invoke external filters

I am very new to programming and this is my first functional code. It works fine but I'm sure that I could use a lot of optimization. If you see any blunders or would be able to help condense the ...
6
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4answers
1k views

Generating DNA sequences and looking for correlations

I've written a script to generate DNA sequences and then count the appearance of each step to see if there is any long range correlation. My program runs really slow for a length 100000 sequence 100 ...
12
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1answer
5k views

Simple DNA sequence finder w/ mismatch tolerance

The goal with this function is to find one DNA sequence within another sequence, with a specified amount of mismatch tolerance. For example: ...
2
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2answers
157 views

Data processing task for bioinformatics

I threw together this C program today to handle a bioinformatics data processing task. The program seems to work correctly, but I wanted to know if anyone has suggestions regarding how the input data ...
5
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2answers
154 views

Finding database matches and storing them in a glycopeptide structure

I am relatively new to C and would like some feedback on a function that I have written, if it adheres to C standards or if there are some other things which I could have done better/differently. <...
9
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6answers
368 views

Analyzing genetic tags

I've gone back and forth a few times recently on my Perl coding style when it comes to module subroutines. If you have an object and you want to call the method bar ...

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