Bioinformatics connects life sciences and quantitative sciences, typically involving the application of software and algorithms to solve computationally intensive questions, such as those in genomics, sequence analysis, and systems biology. Questions tagged Bioinformatics should have a direct ...

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Using the IMGT/GENE-DB service to find RSS

I'm trying to get the data for the Human and Mouse 12 and 23 Recomination Signal Sequences (RSS), to run a classification algorithm on it. I'm not a biologist, so I apologise in advance for my ...
2
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2answers
84 views

Consensus codon optimization by organism

Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables ...
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1answer
83 views

Generating custom human DNA sequences based on traits such as eye colour?

I'm wondering if it would be possible to create software (unless some already exists, but I couldn't find any) to generate human DNA (the base pairs on the double helix) containing genes representing ...
4
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2answers
60 views

Main methods used to predict functional annotations in GO

Can someone provide me some information about the main method used to predict the inferred electronic annotations in Gene Ontology?
12
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1answer
5k views

What is the significance and method behind Ramachandran plots?

My PI showed a Ramachandran plot in class today with minimal explanation, but I'm interested in finding out more. I understand that the Ramachandran plot shows the relation between the omega phi and ...
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3answers
372 views

Source of DNA sequences

I'm working on a project where I am taking DNA sequences and translating the codons into musical notes. I have some good ideas of how to do this, I'm just not sure what sequences to work with. My case ...
6
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3answers
323 views

What's the use of DNA sequencing results?

Suppose I sequence DNA of some organism (a human perhaphs) and now I have the entire DNA "string" - the sequence of nucleotides. What's the use of that? It's just a "string" where nucleotides encode ...
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4answers
1k views

What exactly are computers used for in DNA sequencing?

I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing. There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts. ...
5
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2answers
154 views

First pass protein structure prediction

I'm working with a protein that doesn't have any homology to other proteins so it will likely require ab initio structure prediction. However, since I don't work for a structure prediction lab and I ...
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3answers
101 views

How to create a collection of anonymous sequences for teaching and testing? [closed]

I am looking for a large collection (>1000) of sequence files (eg. FASTA) from any real organism or a tool to create such a collection. The sequence files would be used for teaching and for testing ...
9
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2answers
266 views

How can I pare down a PDB file in Python to only include specific residues?

I'm trying to make a script that will take a MTZ file (reflections), convert it into a CCP4 map, then pare that map down to only encompass a desired area to cut down on the size of my PyMol session ...
6
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1answer
82 views

Is there a tool to find the action of an enzyme in a metabolic pathway?

Is there any tool to search the biochemical action of a particular enzyme in a metabolic pathway of an organism? In other words, how can I find if enzyme "E" is involved in the metabolic pathway for ...
12
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3answers
648 views

Why do restriction enzymes tend to have an even number of bases in their recognition site?

When reading my textbook I noticed that in all examples but one from eight the recognition site was an even number of bases. I wondered if this was just a co-incidence, so I took the data from this ...
3
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1answer
446 views

Displaying nucleotide at a single position from RNA-seq reads in a BAM file

How do I display a single nucleotide position from reads in a BAM file? I have been looking at variation using samtools mpileup, but I want to actually just display the nucleotide at the position I am ...
7
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1answer
117 views

PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?

I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors. I do this by predicting the location of Hydrogens on residues and then calculating how far these ...
9
votes
1answer
417 views

How do I get the current “camera position” in PyMol so I can reuse it in scripts?

I have a few protein models I want to take pictures of with various ligands bound. It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same ...
8
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2answers
907 views

How can rooted and unrooted (phylogenetic) trees be distinguished from one another

I understand that both are similar in structure But how can they be easily identified as one or the other? Is it simply based on the presence or lack of a named root (the root is identified as a ...