61
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I just had my genome sequenced. Can someone tell me what these different file formats are?
This is a great biological question! It asks a lot about how empirical science is done in the field of modern biology. I'm glad we encourage such questions from curious people who want to learn more.
...
- 5,580
27
votes
Accepted
How to convert bwa mem output to BAM format without saving SAM file
For directly outputting a sorted bam file you can use the following:
bwa mem genome.fa reads.fastq | samtools sort -o output.bam -
Optionally using multiple ...
- 386
13
votes
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Computer Virus that infects DNA?
As I understand from your post, the computer virus you are talking about is modifying database (FASTA files) in genetics. That would have a pretty bad impact on research in genetics and medicine.
If ...
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13
votes
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Why should we use the NA12878 dataset for benchmarking?
So to clarify for people unfamiliar with NA12878, that's the sample identification for a particular Utah woman. Her parents are NA12891 and NA12892. In human variation data-sets that's what we are ...
- 837
12
votes
Where can I get a file/list of the common and scientific names of species?
Maybe not a direct answer to your question, depending on what you mean with "unencoded data file", but the Global Biodiversity Information Facility (GBIF) has an API where you extract data for species ...
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12
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Where can I get a file/list of the common and scientific names of species?
Uniprot has a list of the controlled vocabulary for common and scientific names of species listed here.
An example entry:
...
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12
votes
How to convert bwa mem output to BAM format without saving SAM file
Found the solution. You just need to pipe the output from bwa mem into samtools view like so
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- 353
12
votes
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Alternatives to NCBI BLAST during US government shutdowns?
b.nota is correct - Just further adding to his answer. The International Nucleotide Sequence Database Collaboration (INSDC) is a consortium between DNA Data-bank of Japan (DDBJ), EMBL-EBI and NCBI. ...
- 1,621
11
votes
Is it possible to establish a newer animal model completely based on Bioinformatics studies?
It is naïve to think that the extent of protein similarity is sufficient to determine what is the best animal model for a human disease. The physiology of the animal and the question of compensatory ...
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10
votes
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By just looking at an unlabeled picture, how do you know it is a protein?
Shapes
This is a common way of illustrating a protein and is often called a "protein cartoon". There are other common ways of illustrating proteins.
This cartoon shows you where α helices ...
- 11.3k
9
votes
Significance of upper-case, lower-case and Ns in UCSC DNA files
Lowercase letters indicate repeat-masked regions. N's represent gaps.
See:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/S4Sx8UdJAwM/tLTpVVzdhFMJ
- 91
9
votes
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Biological meaning of read length
The read length has absolutely nothing to do with what you are sequencing. It is a characteristic of the sequencing technology you use. NGS sequencing techniques typically produce this sort of short ...
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9
votes
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How are cell death like apoptosis and entropy related?
Unless you have a closed system, don't bother with the second law. These sound like some poetic descriptions but they won't tell you much about biology.
It is argued that cell senescence is due to ...
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9
votes
Can We Determine the Cell Types Ab initio?
No.
Cell types are identified by differential gene expression. Every cell has (effectively) the same genome, but different expression patterns give you different functions.
You could attempt to ...
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8
votes
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Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs
The two most common families of scoring matrices are BLOSUM and PAM. Each of them has a score for every possible alignment combination between the 20 standard amino acids1. They both do more or less ...
- 12.9k
8
votes
What was the first piece of work in computational biology?
I don't believe you'll ever find the first work in bioinformatics (or computational biology, as you put it), however the field really began in the times of accumulating data about protein biochemistry....
- 160
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What was the first piece of work in computational biology?
Another nomination, if you include infectious disease epidemiology as part of biology and hence computational simulations of epidemics as part of computational biology:
Measles periodicity and ...
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8
votes
Accepted
What's cosmic VCF?
VCF is an abbreviation for Variant Call Format. It is a file format for SNPs.
COSMIC stands for Catalogue Of Somatic Mutations In Cancer. It is a database.
Have a look at the links for more ...
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8
votes
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Where can I find large datasets of protein-interaction networks?
There is a bunch of decent protein-protein interaction databases: Biocarta, BioGrid, DIP, InnateDB, IntAct, MINT, PPID.
Some of them aren't available now, but you can download datasets from the ...
- 1,025
8
votes
Accepted
What do the colors mean in representations of amino acids?
There is no ‘standard’ colour scheme for amino acids in the sense of one recommended by a standards or professional organization for biochemists. There are several schemes used in practice — either by ...
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7
votes
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Programs/software to graph biological data
There is no standard software, programming language, or library used for computing and graphing biological data. The R language is commonly used for statistical work, but Python (in conjunction with ...
- 839
7
votes
Accepted
What do the letters 'p' and 'c' mean in mutation descriptions?
According to the HGVS guidelines, a letter prefix should be used to indicate the reference sequence used. Accepted prefixes are:
“g.” for a genomic reference sequence
“m.” for a mitochondrial ...
- 1,025
7
votes
Accepted
Program (on Mac) to show 3D protein structures?
Jmol: how to install
Here are instructions for getting Jmol to run on a Mac (or with a slight variation in the runtime file you need to download and the security warnings, on a PC).
Download Jmol ...
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7
votes
Can two proteins sharing a few domains be considered homologous?
Homology means shared evolutionary ancestry. Sequence similarity is often used as a proxy for homology but inferences should be made with care.
The similarity between two genes/proteins should not ...
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6
votes
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Why did this project encode information in DNA in binary and not in base 4?
In the research article on the effort, they give the following explanation for doubling up nucleotides, rather than have each nucleotide stand for two bits:
This allows us to encode messages many ...
- 1,554
6
votes
Accepted
How the genome assembly be done after k-mer counting?
There are multiple ways of doing genome assembly.
The term you are probably looking for is "De Bruijn-Graph based assembly". Using this you can find a lot more different explanations of how it is done....
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6
votes
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How to batch convert gene names to protein IDs in Uniprot?
ID mapping
This is called ID mapping. It used to be a headache as programmatic sequence comparisons were the only real way, but it is pretty trivial these days.
As mentioned in the comments, by far ...
- 11.3k
6
votes
(Bioinformatics) Protein-Protein Software Prediction
This review about protein docking will hopefully get you started.
Xue, L. C., Dobbs, D., Bonvin, A. M., & Honavar, V. (2015). Computational prediction of protein interfaces: A review of data ...
6
votes
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How valid are GO (Gene Ontology) terms?
There are quite a lot of articles(1,2, etc.) which have investigated this, I think this article did a great job to give a visual representation of the specificity, reliability and coverage:
also ...
- 2,380
6
votes
Accepted
Whole Genome Sequencing vs Whole Exome Sequencing
WES, almost certainly. First of all, the vast majority of phenotype-causing variants are found in exons. For most analyses that are looking into disease causing mutations, WGS is pointless. It only ...
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Only top scored, non community-wiki answers of a minimum length are eligible