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21247
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location Marseille, France
age 34
visits member for 2 years, 2 months
seen 12 hours ago

Elected moderator on Unix & Linux. Feel free to @ping me in chat if there's anything I can help you with.

I am a computational biologist with a background in biology, not computers. My PhD work was on gene prediction and comparative genomics but my current research is in systems biology, specifically protein-protein interaction networks.

profile for terdon on Stack Exchange, a network of free, community-driven Q&A sites


15h
comment Are added yogurt cultures harmful to the gut?
I have no idea what you mean by synthetic bacteria but please don't equate synthetic with harmful and natural with healthy. The most dangerous substances we know are 100% natural. Consider, for example, rattlesnake venom, hydrochloric acid and plutonium.
1d
comment Installing MRBAYES
@Bez that might indeed be best. SO gets enough off topic questions as it is :)
1d
comment Installing MRBAYES
This question appears to be off-topic because it is not about biology.
1d
comment Installing MRBAYES
@Bez this is not on topic on Stack Overflow, it has nothing to do with programming. It would be on topic on Super User or Unix & Linux though. Devinity, consider deleting this and reposting there. If you do, please also provide a link to the MRBAYES archive you downloaded and clarify whether you ran all three commands or only the last. Also make sure you specify whether the ./configure script was successful.
Oct
9
comment If DNA is the input, what is the output?
@canadianer well, you claimed "we actually do understand DNA" and I'd argue that we understand very, very little. Especially when it comes to complex questions like how "different outputs" are chosen (think alt. splicing/choice of splice site/cis+trans regulatory elements/% of genome transcribed/methylome and epigenetics in general etc, etc). We understand the basic mechanics but are still very very far from understanding the regulation.
Oct
9
comment If DNA is the input, what is the output?
You might find this article interesting: ncbi.nlm.nih.gov/pubmed/11504843.
Oct
9
comment If DNA is the input, what is the output?
@canadianer really? That's news to me. We understand a lot about it but not everything. Not even close to everything.
Oct
6
comment Open Source Variant Caller comparable to GATK Haplotype Caller?
You could also try asking on biostars.org.
Sep
30
comment Is Sugar a stimulatant or a weak sedative?
Could you provide a summary of these arguments? It's better to have the answer here rather than on another site which is behind a paywall (not everyone has institutional subscriptions)
Sep
29
comment What is the difference between a fixed substitution and a single nucleotide polymorphism (SNP)?
I'd need more context to be sure but what makes you think that the substitutions were only a single nt? Also, that sentence could be read as having found 464 SNPs, of which 430 were fixed.
Sep
24
comment Which C. elegans would be appropriate for general study?
What question do you want to answer? The "appropriate" decision will depend on what exactly you want to investigate. What conclusions will you want to draw from your research?
Sep
23
comment Does this “fleeing spiders leaving fields of webs” phenomenon have a name?
I doubt it will be called anything specific. It's just spiders fleeing a flood like any other animal.
Sep
22
comment BLASTn vs ORF tools
@Raghavakrishna I'm sorry but I still don't understand. The details always depend on what you're actually doing. If BLAST gives you a hit, then that's a hit. Whether or not that is biologically relevant is another question and I can't answer that unless I know what question you are asking.
Sep
21
comment BLASTn vs ORF tools
@Raghavakrishna why would they be false positives because they align against the - strand?
Sep
19
comment Finding proteins in DNA sequence
@Raghavakrishna I still don't understand what you're asking. Sequencing projects sequence one strand and call that the + strand and then extrapolate the sequence of the - strand. If you have a question about this, please ask a new question so you can explain it clearly and get a full answer.
Sep
19
comment Finding proteins in DNA sequence
@Raghavakrishna what do you mean? What method? If you mean the two tools I mentioned, exonerate searches both strands by default and genewise does so if you give it the -trev flag.
Sep
16
comment Why aren't introns found on the ends of pre-RNA?
@user137 exactly. Being an exon has nothing whatsoever to do with being a coding exon. You even have transcripts that don't code for protein at all but that contain introns regardless.
Sep
16
comment Why aren't introns found on the ends of pre-RNA?
@user137 (and Armatus) UTRs are exons, some of them even contain introns and are spliced just like coding exons.
Sep
6
comment Degenerate Alignment Analysis
This would be much easier to answer if you gave us some more context. Presumably you are referring to sequence alignments but where did you read the term? What was it referring to?
Sep
4
comment Did Darwin ever reach the conclusion that selection will remove variation?
I don't think you can simply ignore mutation like that. Each generation may have its variation reduced by selection but novel variants will also pop up through mutation and copy errors. We'd have to take both rates (that of loss and that of gain of variation) into account to answer this.