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Bioinformatics

Proposed Q&A site for every life sciences researcher, from biologists to clinicians through computer scientists
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Announcements

8  
Huh. There were lots of comments here, most of them pointing to BioStar (biostar.stackexchange.com). What happened to them? – Michael Kuhn Jun 16 '11 at 14:20
2  
@biocs note that these are titled "ANNOUNCEMENTS" now, so hopefully you can guess why... – Jeff Atwood♦ Jul 1 '11 at 19:14
6  
a paper on Biostar has been published on PLoS Computational Biology: ploscompbiol.org/article/… – dalloliogm Oct 28 '11 at 14:52
show 6 more announcements
2
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4
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Neuroinformatics a subset of Bioinformatics?

feb 9 at 4:44 Nolan Nichols 91
20
votes
5
answers

Successor to BioStar

dec 29 at 3:02 Kevin Vermeer 338
8
votes
2
answers

Healthcare IT Site: Reality Check

sep 12 at 23:21 xiaohouzi79 405
3
votes
0
answers

Is the Bioinformatics description too broad?

aug 15 at 23:55 EpiGrad 628

create new discussion

This proposal is now in the Commitment phase — example questions are locked!

37 Example Questions (7 closed)

active oldest votes
up vote 22 down vote
Where can I get the entire human genome sequence? And the sequences of particular genes?
added by Pedro Lopes Jun 17 '10 at 14:45
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up vote 20 down vote
Is anyone aware of existing genomic variation sites? Where can I find variants for a specific gene?
added by Pedro Lopes Jun 17 '10 at 14:47
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up vote 20 down vote
What are the most actively developed biological databases?
added by miku, edited by WikiSpeedia hang-around Nov 25 '10 at 22:04
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up vote 20 down vote
What are the differences between different BLAST substitution matrices (e.g. BLOSUM 62)?
added by Dana Robinson Jul 7 '10 at 7:26
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up vote 20 down vote
What are the differences between BLAST and PSI-BLAST?
added by llukas Jul 21 '10 at 23:27
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up vote 17 down vote
Where can I get 3-way species alignments?
added by Ron Gejman Jun 18 '10 at 22:35
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up vote 15 down vote
What is the best web-service to perform a BLAST analysis?
added by Pedro Lopes Jun 17 '10 at 14:44
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up vote 7 down vote
What are some good peptide/protein validation algorithms for identifying MS/MS spectra?
added by nicorellius Jun 24 '10 at 19:57
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up vote 5 down vote
What is the difference between Smith/Waterman sequence alignment and Needleman/Wunsch sequence alignment?
added by Daniel Standage Feb 10 '11 at 12:25
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up vote 4 down vote
How can I map gene, protein (or other) IDs from [database or resource] to [database or resource]?
added by Unode Nov 12 '10 at 0:29
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up vote 4 down vote
Is there any library in VC++ which helps to preview molecule using OpenGL?
added by Csabi, edited by WikiSpeedia hang-around Mar 23 '11 at 20:48
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up vote 4 down vote
What are the best papers for using succinct data structures in genome assembly?
added by Alex Bowe Mar 22 '11 at 0:24
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up vote 4 down vote
Where is the difference between MAS5 and RMA normalisation of microarray data? Which is when more appropriate?
added by Torbjoern Apr 20 '11 at 5:37
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up vote 3 down vote
I need the EBI NRDB protein database as it was in 1998. Is it possible to get it?
added by WikiSpeedia hang-around Jun 18 '10 at 21:49
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(EBI NRDB database: non-redundant protein sequence database.) – WikiSpeedia hang-around Jun 18 '10 at 21:50
The question could probably be posed in a more elegant way. I am open for suggestions. – WikiSpeedia hang-around Jun 18 '10 at 21:50
up vote 3 down vote
I am a programmer, and I'd like to start working in the bioinformatics field. What is the best way to get the skills that will let me get a job?
added by Sergey Aldoukhov, edited by WikiSpeedia hang-around Nov 25 '10 at 21:56
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Given this question has (almost) even on-topic and off-topic votes, I believe it's quite important to discuss why the votes. I, personally, believe that documentation/learning tools for any field are on topic for such field. This question, however, is too broad and argumentative, making almost impossible to select a correct answer. – Aleadam May 28 '11 at 6:09
up vote 3 down vote
What is your recommended RNA-seq alignment pipeline?
added by GWW Nov 25 '10 at 1:10
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up vote 3 down vote
What data mining tools are useful in bioinformatics (as an application)?
added by Shankarooni, edited by WikiSpeedia hang-around Mar 8 '11 at 23:24
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The question is too broad. – Tim N Feb 7 '11 at 22:14
might become an FAQ though - if maintained properly – Ronald May 20 '11 at 0:55
I flagged as not a good example. It could be on topic, but as Tim said is too broad and, even worst, the answer will change with time, so the only way I see value in this question is as a wiki list. – Aleadam May 28 '11 at 4:29
up vote 3 down vote
Do current data sets on the human genome have valid data in non-coding regions? Is there a database that has non-coding region sequences?
added by dorkusmonkey Dec 3 '10 at 17:59
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up vote 2 down vote
What is the best way for merging SNP rsid with Genes Ensemble id?
added by chl Dec 18 '10 at 20:13
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up vote 2 down vote
What are some good resources for setting up a computational model of auxin expression in Arabidopsis?
added by smithco Feb 18 '11 at 7:17
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up vote 2 down vote
Given a datafile with a matrix with individuals on rows, and measurements on columns, what's the algorithm for the Mahalanobis square distance?
added by Victor Jalencas, edited by WikiSpeedia hang-around Apr 5 '11 at 20:46
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from the population of all samples to a given individual, that is. This question illustrates that bionformatics is not only biochemistry and genomics, but also demography, for example. – Victor Jalencas Mar 22 '11 at 0:25
up vote 2 down vote
Which are the most used tools for mRNA secondary structure prediction and what are the differences between them?
added by Zenon May 27 '11 at 0:40
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up vote 1 down vote
What parameters/values (FC, IQR, etc.) do you use for filtering differentially expressed genes in microarray analysis?
added by kriegar, edited by WikiSpeedia hang-around Apr 5 '11 at 20:45
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up vote 1 down vote
Is there a Java API to query NCBI databases (PubMed and PubChem)?
added by Aleadam, edited by WikiSpeedia hang-around Jun 8 '11 at 14:11
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up vote 1 down vote
What's the best way to quantitate samples for deep-sequencing?
added by weronika Jun 17 '11 at 5:37
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up vote 1 down vote
How do I manually define peaks on the results from an Agilent bioanalyzer DNA chip?
added by weronika Jun 17 '11 at 6:50
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up vote 0 down vote
I have a timeout problem for very large Mascot results. Is there a solution? [closed]
added by WikiSpeedia hang-around Jun 18 '10 at 21:45
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closed as off topic by footie11, fgibson, Martin Peters, Edgar, blueberryfields Dec 3 '10 at 22:09

This question does not relate to the topic of the proposal.
It was closed as part of an automated migration of off-topic to close votes on September 29, 2011.

(Mascot: en.wikipedia.org/wiki/Mascot_%28software%29) – WikiSpeedia hang-around Jun 18 '10 at 21:46
up vote 0 down vote
How many cells are in the human body? Can a DNA encode a quantitative information, if yes - how? [closed]
added by psihodelia Feb 9 '11 at 13:10
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closed as off topic by kriegar, Pierre, Zenon, Gagravarr, Dori May 29 '11 at 23:11

This question does not relate to the topic of the proposal.
It was closed as part of an automated migration of off-topic to close votes on September 29, 2011.

up vote 0 down vote
How do I use ImageJ to quantify the bands intensity in a Western blot?
added by Aleadam May 28 '11 at 4:40
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up vote 0 down vote
What's the best command-line tool for adapter stripping from Illumina paired-end deep-sequencing data?
added by weronika Jun 17 '11 at 5:41
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up vote 0 down vote
How do I install Windows operating system on my computer that runs my Mass Spectrometer?
added by fgibson Jun 22 '11 at 10:58
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up vote -1 down vote
What is the chemical structure of caffeine and what diseases can it cure? [closed]
added by fgibson Aug 25 '10 at 10:59
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closed as off topic by Christian, Edgar, whsqwghlm, Tangurena, blueberryfields Dec 3 '10 at 22:09

This question does not relate to the topic of the proposal.
It was closed as part of an automated migration of off-topic to close votes on September 29, 2011.

Part of this question (chemical structure) could go to the Biology site when it launches. – ogerard May 28 '11 at 6:22
up vote -1 down vote
Where can I get my own genome sequenced and analyzed? [closed]
added by blueberryfields Dec 3 '10 at 0:45
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closed as off topic by ogerard, Aleadam, Simon Cockell, weronika, Casey Bergman Jun 22 '11 at 9:42

This question does not relate to the topic of the proposal.
It was closed as part of an automated migration of off-topic to close votes on September 29, 2011.

I suppose this is not a good question for researchers... – Zenon May 27 '11 at 0:41
up vote -1 down vote
Does the panspermia hypothesis have any information-theoretic backing? [closed]
added by blueberryfields Dec 9 '10 at 15:40
link|flag

closed as off topic by dalloliogm, Ronald, Aleadam, Gagravarr, mbq Jun 8 '11 at 13:57

This question does not relate to the topic of the proposal.
It was closed as part of an automated migration of off-topic to close votes on September 29, 2011.

up vote -1 down vote
How do I identify protein coding domains X, Y, and Z in a genome?
added by opierce Mar 22 '11 at 0:41
link|flag
What genome? To be answerable, this question should be much more focused. – Aleadam May 28 '11 at 4:31
up vote -2 down vote
I'm trying to use BIOMART web services, however I can't get a connection... Any ideas? [closed]
added by Pedro Lopes Jun 17 '10 at 14:48
link|flag

closed as off topic by Heath Hunnicutt, fgibson, Martin Peters, warren, Edgar Nov 20 '10 at 8:24

This question does not relate to the topic of the proposal.
It was closed as part of an automated migration of off-topic to close votes on September 29, 2011.

2  
wait and try later ;-) – neilfws Jul 16 '10 at 7:51
up vote -13 down vote
What is the meaning of life? [closed]
added by Pedro Lopes Jun 17 '10 at 14:57
link|flag

closed as off topic by jmanning2k, Kyra, Stefano Borini, nicorellius, Felipe Knorr Kuhn Jun 27 '10 at 23:59

This question does not relate to the topic of the proposal.
It was closed as part of an automated migration of off-topic to close votes on September 29, 2011.

5  
Off topic example should be what we don't want to be discuss on site, but close enough. This is totally unrelated. – Guillaume Coté Jan 27 '11 at 23:14
However, don't be surprised if this topic is touched upon in many ways quite often ;) – WaxWing May 4 '11 at 10:32

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