Questions tagged [bioinformatics]

The science of collecting and analyzing complex biological data such as genetic codes using informatics.

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36
votes
3answers
83k views

What is the difference between local and global sequence alignments?

There are a bunch of different alignment tools out there, and I don't want to get bogged down in the maths behind them as this not only between software but varies from software version to version. ...
11
votes
1answer
759 views

Sequence evolution simulation tool

I'm looking for a tool to simulate sequence evolution given a specific mutation model and birth-death model. I'm aware of tools and packages like INDELible, Seq-Gen and PhyloSim, but they simulate ...
156
votes
7answers
16k views

Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? How about GOTO?

Does DNA have anything like IF-statements, GOTO-jumps, or WHILE loops? In software development, these constructs have the following functions: IF-statements: An IF statement executes the code in a ...
9
votes
2answers
5k views

How to find miRNA binding sites on a specific gene?

I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? ...
7
votes
2answers
6k views

Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs

The Wikipedia page on BLAST states that: The scores are created by comparing the word in the list in step 2* with all the 3-letter words. By using the scoring matrix (substitution matrix) to score ...
5
votes
3answers
586 views

What is the state-of-the-art algorithm for multiple sequence alignment?

Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment? How big is the need for better algorithms? How many sequences need to be alignment in a ...
9
votes
2answers
357 views

Can forensic DNA analysis be used to generate a visual approximation of a suspect?

In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
4
votes
1answer
94 views

Why do we need two markers to measure a recombination rate?

In calculating recombination, Why is it necessary to take into account pairs of loci where one marker is heterozygous? Why is it necessary to take into account pairs of loci where both markers are ...
8
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4answers
2k views

Suitable introductory book on Bioinformatics for a computer scientist?

Do you have any suggestions on a suitable introductory text on bioinformatics for a computer scientist? Any recommendations with pros and cons of different books would be appreciated. I'm mainly ...
10
votes
1answer
992 views

Has any large-scale origin-of-life simulation/experiment been done?

I have been thinking a little about the origins of life, and was further inspired by this question: How did the first self replicating organism come into existence? I can accept that we don't quite ...
10
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2answers
231 views

What role does a protein's size have on protein-protein interactions?

Protein-protein interactions are when two or more proteins bind together, possibly for some important biological function. Recently, I'm starting to look more into proteins, and in particular, ...
-1
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1answer
2k views

basic programming and bioinformatics [closed]

As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work ...
6
votes
3answers
285 views

How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: how ...
2
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1answer
7k views

What are Codominant vs Dominant Genetic Markers?

When talking about types of genetic markers, the adjective "dominant" and "codominant" are often used. I don't fully understand their definitions and found contradicting definitions. Foll and ...
10
votes
3answers
516 views

How do we know if the folding@home project results are right?

Some of us are involved in the folding@home project, spending time, money, and resources. I would like to know the answer to two main questions: How do we know we fold it right? I mean, these models ...
8
votes
2answers
2k views

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

I understand that rooted and unrooted phylogenetic trees 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 ...
3
votes
2answers
941 views

Local BLAST Copy Number per Hit

I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at e-values,...
48
votes
4answers
7k 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. ...
12
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5answers
742 views

Introductory literature for synthetic / systems biology

I am a computer engineer (MSc in Computer Engineering) who's looking to switch into the field of synthetic / systems biology. I have a comprehensive layman's understanding of evolution, genetics, ...
10
votes
5answers
32k views

What E-value BLAST cut-off is best?

What is the best cut-off for e-value in BLAST? Some say 0.01 ,others 0.0001? Even BLAST tutorials don't give a very clear idea about which cutoff suits which purpose? Could some experts give me a ...
9
votes
1answer
10k views

Difference between strand-specific and not strand-specific RNA-seq data

I would like to ask the difference between strand-specific and not strand-specific dataset. As far as I know, strand-specific data means that we know which strand the transcript is from. I do not ...
9
votes
2answers
2k views

What are we missing about the real workings of the evolutionary process? [closed]

As a scientist (and a computer scientist at that) my view is that if we cannot simulate a process we have not understood it properly. I have been following the interesting field of Artificial Life for ...
21
votes
4answers
859 views

Machine learning for light microscopy — problems to solve?

I would like solve some biological problems that would improve the state-of-the-art of biology or bioinformatics. In particular, I want to apply machine learning on light microscopic images. The ...
14
votes
4answers
2k views

Where can I get a file/list of the common and scientific names of species?

I am searching for an un-encoded data file with common and scientific names for example of a few hundred species or tens of thousands, where I can search the common and scientific labels of organisms.
11
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2answers
839 views

Books on machine learning applications in Biology

I have recently engaged with a collaboration, which requires me to construct, then train an unsupervised artificial neural network (ANN). However, I have only a very coarse understanding of what ...
4
votes
1answer
445 views

Visualising a subset of the tree of life

I understand that many curated trees of life already exist (eg http://tolweb.org/tree/) but is there any website that allows one to input a list of organisms, and then produce the current best guess ...
14
votes
2answers
1k views

Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein ...
13
votes
1answer
945 views

Human disease and associated phenotype database?

Does anyone know of any good databases that contain symptoms for diseases and other ailments in humans? I've tried working with UMLS, but thats been impossible to work with. I've also tried working ...
8
votes
1answer
84 views

Downloadable worldwide database of disease statistics?

I am looking for a downloadable database of disease statistics. I have emailed the good folks over at HealthMap, but they haven't gotten back to me yet. As far as I can tell, their data relevant to ...
7
votes
2answers
12k views

What does phasing mean?

What does phasing mean in genetics/informatics? I've heard that a phased file is a file that has genes separated by chromosome, but can someone give a concrete definition of what phasing actually ...
6
votes
1answer
1k views

What is the last heavy atom of an amino acid?

I'm a electrical engineer and I'm learning about bioinformatics. I was reading this paper that uses the last heavy atom to search for active sites of a protein but what would be a heavy atom? Is it ...
5
votes
1answer
179 views

Learn Bioconductor the hard way!

I came to analyzing population genetics data from the background of a theoretician and a computer biologist but not with the standard tools that a bioinformatician (or empiricist in population ...
7
votes
2answers
958 views

introduction to Chip Seq

I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've ...
5
votes
2answers
1k views

How to use Autodock just for (re)scoring

I have some protein-ligand complexed that I have been docking with some other software and just want to use Autodock to evaluate those complexes. So, basically I just want to use it as a scoring ...
4
votes
1answer
1k views

How to do multiple sequence alignment?

I have a DNA sequence that makes protein 1. but now I have asked to: compare the amino acid sequence of protein 1 with nine homologous proteins and make a multi sequence alignment (MSA) of the ...
4
votes
1answer
1k views

Why is ab initio protein secondary structure prediction less reliable than alternatives?

To predict secondary structure of proteins three types of Algorithms are used Ab initio, homology based and neural networks. Among these neural networks prove to be more accurate and give good results ...
4
votes
3answers
403 views

What could I call such nucleic-acid-Sequence? A sort of palindromic sequence? is there any term called mirror repeat?

5'... ATGCC|CCGTA ...3' 3'... TACGG|GGCAT ...5' or say 5'... AAGT|TGAA ...3' 3'... TTCA|ACTT ...5' or in generalised way; on each strand; ABCDEF|FEDCBA Is there any terminology for such-sort ...
3
votes
1answer
2k views

best book for a comprehensive introduction to biology for a computer science graduate interested in undertaking research in bioinformatics [closed]

I have a postgraduate degree in computer science, and I wish to undertake research in bioinformatics. I had chemistry but no biology in high school. I have read bioinformatics books like "biological ...
3
votes
1answer
2k views

Plastid and mitochondria

I am not a biologist, so please bear with me for this basic question. Although I tried googling, I am confused. What is the difference between plastids, chloroplasts and mitochondria? Are there any ...
1
vote
1answer
550 views

How to write a palindrome sequence as-wish (create, theoretically) ? (self-answered)

There are specific examples from nature, of palindromic sequences. But without memorizing them, is there any way to randomly write or create or derive a palindromic sequence for a theoretical ...
1
vote
1answer
91 views

How to selectively download 3 fields from every record in UniProtKB?

I want to download a comprehensive table of protein names from uniprot.org. More precisely, I want to generate a tab-delimited table consisting of the id (...
14
votes
1answer
1k 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 ...
10
votes
1answer
2k views

Mass spectrometry versus western blotting for validation

I have mass spectrometry data (LC-MS/MS) from rat cortices under either drug or control treatments. The results were performed in triplicate (three pairs of rats, drug or control per pair). In ...
8
votes
5answers
1k views

Book/source for learning bioinformatics, focused on genomics?

Does anyone know of sources for learning bioinformatics, focused on genomics? I would like to learn alot of skills I could apply potently in the workforce if I ever became adept at the fields. My ...
5
votes
1answer
695 views

Software for counting fly eggs

Is there any software that could be used to rapidly (quicker than humans) count the eggs laid by Drosophila on a substrate by placing them under a microscope with a camera attached? The eggs are laid ...
5
votes
3answers
186 views

Finding a template/oligo combination for my first PCR experiment

I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine. Everything is done now and I ...
3
votes
0answers
166 views

Good poly-A filtering rules or tools

I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have ...
3
votes
0answers
49 views

How much Open Access Data is there in genetics? [closed]

Type of data of interest I would like to consider Genetics data (SNP, microsatelites, whole genome sequencing, RFLP, ...) Genetic - phenotype data (disease-related data, QTL, etc...) Sequence ...
3
votes
1answer
2k views

Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?

Why are the amino acids - cysteine and tyrosine used in isoelectric point calculations for a protein sequence, yet neither of them are positively charged molecules? and are not used in net charge ...
3
votes
1answer
70 views

Rigorous definition of the kinship coefficient and proof of a recursion thereof

I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for ...