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Bioinformatics

Proposed Q&A site for students, developers, teachers, users, researchers and others interested in bioinformatics.
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44 Example Questions

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up vote 23 down vote
Does there exist programming languages that have specific features that are useful for bioinformatics?
added by wythagoras Mar 31 '16 at 12:50
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1  
One would have to define what "useful for bioinformatics" means, precisely, otherwise this one is opinion-based and should be closed. – Raphael Jun 13 '16 at 8:37
Core packages of the R programming language, includes Bioconductor. Also, the bioinformatics communities I have worked with, the members are often working on some sort of methods paper to be later added to R's collection. MATLAB, since 2010-ish added a "Bioinformatics ToolBox" library. Providing GUIs and elaborate code for wrangling common tasks. Python's Biopython and PyCogent wrappers are also very well known. – hello_there_andy Mar 16 at 23:18
up vote 16 down vote
How is a consensus sequence typically created?
added by Franck Dernoncourt Mar 30 '16 at 23:06
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up vote 16 down vote
What are some basic differences between fasta and fastq file?
added by manetsus Apr 16 '16 at 17:07
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Just from memory, fastq has quality statistics of the original sequencing method – hello_there_andy Mar 16 at 23:20
up vote 15 down vote
How to design an algorithm that finds the begin of an mRNA string that codes for a protein in Python?
added by wythagoras Mar 31 '16 at 12:52
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There are two questions here, really. 1) Algorithm design (--> [cs.SE]) and 2) implementation (--> [SO]). As such, it's also too broad. – Raphael Jun 13 '16 at 8:33
@Raphael Changed to design an algorithm – wythagoras Jun 13 '16 at 11:25
up vote 13 down vote
What is the difference between biostatistics and bioinformatics?
added by Franck Dernoncourt Mar 30 '16 at 23:06
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up vote 11 down vote
How much memory is required to store human DNA?
added by kenorb Apr 18 '16 at 9:07
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This is an easy exercise with a calculator. – Raphael Jun 13 '16 at 8:34
6  
@Raphael answers may also handle compression techniques, if some of them are specific to DNA sequences. – svavil Oct 7 '16 at 20:54
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Without considering pattern-based compression techniques like LZ77, you can represent the 4 DNA nucleotides with 2 bits. So it's just 2 bits * 3,234,830,000 (base pairs / haploid human genome) * 2 (haploid/diploid) / 8 (bits/byte) = 1.6174 GB / diploid human genome. – Ian Harvey yesterday
up vote 10 down vote
How to emulate a protein behavior ?
added by Me Good Guy Apr 6 '16 at 11:29
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up vote 10 down vote
How to convert fasta files (.fa) to gtf files for transcript?
added by kenorb Apr 18 '16 at 9:02
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up vote 10 down vote
How to highlight GLYCINE residues in my Ramachandran plot?
added by kenorb Apr 18 '16 at 9:03
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up vote 10 down vote
How to find unique DNA/protein sequences of a given length that does not match to any region of the C (elegans genome)?
added by kenorb Apr 18 '16 at 9:06
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Probably ontopic on [cs.SE]. – Raphael Jun 13 '16 at 8:35
up vote 10 down vote
How the genome assembly be done after k-mer counting?
added by manetsus Apr 18 '16 at 13:10
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up vote 10 down vote
How can the study of Bioinformatics increase the future effectiveness of immunotherapy?
added by Mary Johnson May 17 '16 at 15:25
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Speculative and opinion-based. – Raphael Jun 13 '16 at 8:34
@Raphael unless specific past examples can be provided. – svavil Oct 7 '16 at 20:56
up vote 10 down vote
What is the difference between mapper and aligner?
added by manetsus Sep 5 '16 at 5:44
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up vote 10 down vote
What are state-of-the-art algorithms for alignment of MALDI-TOF mass spectra for peptides?
added by liori Sep 26 '16 at 21:21
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up vote 10 down vote
Is there a tool to convert genomic coordinates between different releases of C. elegans reference genomes?
added by bli Nov 21 '16 at 14:28
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up vote 10 down vote
What are the best tools available to use RNA and DNA assembling ?
added by Thisaru Guruge Dec 6 '16 at 11:53
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up vote 10 down vote
What is the difference between a transcriptome and a genome
added by Thisaru Guruge Dec 6 '16 at 11:56
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up vote 10 down vote
What is the tss_id attribute in some gtf files? How is it determined?
added by bli Dec 7 '16 at 18:15
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up vote 10 down vote
How to efficiently generate a random sample of alignments from a bam file?
added by bli Jan 5 at 15:22
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up vote 10 down vote
Are there any rolling hash functions that will hash a DNA sequence and its reverse complement to the same value?
added by Daniel Standage Mar 1 at 16:57
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up vote 10 down vote
If I place genes randomly on a chromosome sequence, how should the distribution of the lengths of the intergenic sequences be modeled?
added by Daniel Standage Mar 1 at 17:01
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up vote 10 down vote
Given a large set of genes from an organism, how can I easily discover their orthologues?
added by yochannah Mar 2 at 14:54
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up vote 6 down vote
What file type do I use for an unannotated complete genome sequence?
added by VeenaG Feb 9 at 13:08
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up vote 4 down vote
How to optimize my recursive function to find the best score for DNA strands?
added by kenorb Apr 18 '16 at 9:04
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1  
Ontopic on [cs.SE]. – Raphael Jun 13 '16 at 8:35
up vote 4 down vote
Are there any open source graphical fragment assembly format (GFA) parsers implemented in Python?
added by Daniel Standage Mar 1 at 17:05
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up vote 1 down vote
What are some applications of read-reference sequence mapping?
added by manetsus Sep 25 '16 at 3:46
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up vote 1 down vote
Should I get a reference genome and annotations from Ensembl, UCSC, or a specific organism-related database?
added by bli Nov 21 '16 at 14:15
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up vote 1 down vote
How can I access to the normalized read count values corresponding to my raw input in a DESeq2 result?
added by bli Nov 21 '16 at 14:21
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up vote 1 down vote
Differences between .fasta and .fastq files?
added by Thisaru Guruge Dec 18 '16 at 18:27
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up vote 1 down vote
Can De-Brujin graphs generate accurate results?
added by Thisaru Guruge Jan 17 at 4:46
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up vote 1 down vote
How can I annotate alternative splicing events without explicitly looking for differential splicing?
added by Daniel Standage Mar 1 at 16:54
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up vote 1 down vote
What is the difference between overlap layout consensus and De Bruijn graphs when performing a de novo assembly?
added by Dylan Lawrence yesterday
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up vote 1 down vote
I'm interested in calling variants using DeepVariant. At this time is it possible to run DeepVariant locally?
added by Greg yesterday
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up vote 1 down vote
I'm interested in formatting my data using the graph genome paradigm. What are the drawbacks of this approach compared to the linear representation?
added by Greg yesterday
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up vote 1 down vote
What is the best way to select coding regions from multiple gVCFs that are on the order of terabytes?
added by Greg yesterday
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up vote 1 down vote
What are the standard quality control procedures when working with whole genome sequencing data from a HiSeq 4000?
added by Greg yesterday
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up vote 1 down vote
Under what circumstances should I use a linear mixed model for conducting a genome-wide association study?
added by Greg yesterday
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up vote 0 down vote
What properties/attributes and methods should I include in a cell superclass?
added by Jenny T-Type May 26 '16 at 1:53
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This seems too broad to me. Shouldn't it depend on the usage intended for this superclass? – bli Nov 21 '16 at 14:24
up vote 0 down vote
When I'm enriching a list of genes, what type of correction should I choose (if any) and why?
added by yochannah Mar 2 at 15:13
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up vote 0 down vote
What sources should I follow to stay up-to-date about PPI prediction methods? What are some good reviews to read about this topic?
added by Zubo Mar 13 at 15:56
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