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Old 04-16-2010, 04:46 AM   #1
Beginner
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Unhappy de novo... beginner questions.

Hello,

I'm a beginenr in bioinformatics and I would like to know what is exactly a de novo discovery. I am using CisGenome in order to process chip-seq data (but we dont care). I show you the extract of my doc (for CisGenome using):

"Motif analysis
A de novo motif search may return multiple motifs. CisGenome identifies the functionally relevant ones by comparing the occurrence rates of the motifs in binding regions to those in matching genomic control regions(ref.37)."
I give you ref.37 : [PubMed: 15297614] if you need it

Do you know where can I find docs in order to understand clearly what a "de novo discovery" is and its usefullness in chip-seq data processing.

while(question==idiot)
{
ban questionner
}
oh no please....

Last edited by Beginner; 04-16-2010 at 04:49 AM.
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Old 04-16-2010, 05:41 AM   #2
krobison
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de novo means without reference to the pre-existing.

In this case, it means taking a bunch of data and inferring a motif without having a prior model for that motif.

Quite commonly in this space "de novo" is shorthand for "de novo assembly" -- assembling a genome which has never been assembled before.

"de novo transcriptome" means assembling the mRNAs with neither prior mRNA nor genome as a guide.
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Old 04-16-2010, 06:03 AM   #3
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Thank you for the answer. But, how is it possible to assembly sequences without a reference. By an algorithm which detects overlapping sequences (ChIP-seq data)?

Good week,

Last edited by Beginner; 04-20-2010 at 01:51 AM.
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Old 04-18-2010, 11:26 PM   #4
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Question

In fact, I'm learning more and more about Chip-seq processing and I believe that de novo discovering is only for RNA-seq and not for chip-seq, isn't it?
Do you agree with?

thanks!

Last edited by Beginner; 04-20-2010 at 04:43 AM.
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Old 04-20-2010, 07:28 AM   #5
ECO
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Hey beginner.

Please do some reading/searching before asking such basic questions. And also please refrain from using "wtf" in thread titles. I like to think we try to maintain a semblance of professionalism here.

Thanks!
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Old 04-20-2010, 11:38 PM   #6
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Exclamation

Sorry,

I just want to bring a bit of madness in this serious world...
Without joking, I understand what you mean and I'll be more serious.

Just a thing, you can't say I have to search information because, that's what I do every days. That's just I'm a beginner (2 weeks I started my traineeship) and I have not a very good english knowledge. Whereas publications are all in english. Moreover, if the base is not understand, no need to go furhter. If you don't want help me, I can understand it but don't say I don't have to ask basic questions here.

Maybe there is a level of knowledge which is needed before registering, but I'm not informed. If it's the case please don't take in consideration what I said.

On one hand, please be comprehensive.
On the other hand, I'll try to ask more pertinent questions.

Have a good day,

Beginner

Last edited by Beginner; 04-20-2010 at 11:41 PM.
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Old 04-21-2010, 06:50 AM   #7
Joann
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Default different approaches to learning

Hi Beginner,

I have some tips for you to get up-to-date basic information that may help to capture your interest in this field--at least until you are more comfortable with your scientific English and the technology. First of all use Google a lot. Don't be afraid to key in scientific terms that confuse you, just give it a go and select the easiest hits for you to read and judge for yourself when you discover inconsistencies in them--and you will.

Also, using these words in a Google Image search picks up a variety of illustrations--see how some are much better or worse than others at explaining the science at hand with few words. Save the best images you find for future reference and maybe for use in your own slides in future talks you may give. Be sure to credit the sources.
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Old 04-21-2010, 10:47 PM   #8
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Google Image is not a bad idea...
Thanks for the tip
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Old 03-22-2011, 01:01 PM   #9
acyc
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Quote:
Originally Posted by krobison View Post
de novo means without reference to the pre-existing.

In this case, it means taking a bunch of data and inferring a motif without having a prior model for that motif.

Quite commonly in this space "de novo" is shorthand for "de novo assembly" -- assembling a genome which has never been assembled before.

"de novo transcriptome" means assembling the mRNAs with neither prior mRNA nor genome as a guide.
there are de novo motif scanning programs for identifying TF binding sites.
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Old 04-27-2012, 03:36 AM   #10
shal
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Quote:
Originally Posted by Joann View Post
Hi Beginner,

I have some tips for you to get up-to-date basic information that may help to capture your interest in this field--at least until you are more comfortable with your scientific English and the technology. First of all use Google a lot. Don't be afraid to key in scientific terms that confuse you, just give it a go and select the easiest hits for you to read and judge for yourself when you discover inconsistencies in them--and you will.

Also, using these words in a Google Image search picks up a variety of illustrations--see how some are much better or worse than others at explaining the science at hand with few words. Save the best images you find for future reference and maybe for use in your own slides in future talks you may give. Be sure to credit the sources.
That's the wonderful idea!! Thanx a tonn!!

regards
s
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Old 06-06-2012, 03:42 AM   #11
shal
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Hi Folks!!

I awaiting the sequencing data (FASTQ) files yet. Can some one please suggest me How can I get my hands in de novo now?

Can some one please suggest me some practice things for de novo genome sequencing? Where I get some raw FastQ files and I carry out all the steps by myself on it.

What should/can I do apart from reading before I get the data?

Thanks and regards
Shal
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Old 04-11-2013, 08:13 PM   #12
afif
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Default De novo sequencing of a halophyte grass

Hi
I am working on a halophyte grass with an estimated genome of 340Mb and 10chromosomes. I have performed the trascriptome sequencing using RNA extracted from leaf and root of control and stressed plants. The The bioinfo analysis of the reds from 454 and illumina showed that this plant is very near to sorghum. Since I am interested in the promoters of salt regulated genes I would like to perform Denovo genome sequencing. Can any one help me for the choice of the best strategy that I should follow to get the best results??? I have the idea to sequence paired-end fragments (PE) using 454 and illumina platform then using sorghum genome and the results of the RNAseq (that I have obtained) to do the assembly Is it the best way???
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