Bernardo Bello Ortí

12 Questions 6 Answers 0 Followers

Questions related from Bernardo Bello Ortí

Which tools are there to find non-coding RNAs in bacterial RNA-seq data?

I'm looking for tools to semi-automate finding non-coding RNAs in bacterial RNA-seq data. I've been able to find some tools but I'm still quite lost (see link below). I've also seen this Biostar...

03 March 2014 4,250 2 View

Is it possible to have a 200 fold change miRNA?

We found a 200 fold change regulation (with good read coverages). Has anyone observed this?

03 March 2014 2,080 5 View

How can I identify pseudogenes in prokaryotic genomes?

I would like to perform whole genome identification of pseudogenes. Could anyone suggest a good strategy?

02 February 2014 3,144 2 View

Locate amino acids in 3D protein structure?

Hi community, I would like to know how to locate a certain protein sequence in the whole protein 3D structure. We are trying to see if these short protein sequences are located on the surface. I...

02 February 2014 4,314 10 View

Can anyone help with batch predict membrane-related genes?

I need to predict membrane-related genes in a 2000 genes list. Could anyone suggest an appropriate approach? I've already filtered out the ones retrieved with GO terms, so this way has already...

02 February 2014 6,652 2 View

What is the difference between txid738 [Organism:noexp] and txid73 8[Organism:exp] filters?

What's the difference between these two filtering alternatives when looking for all proteins available for a selected organism in NCBI? I get the double of proteins in 'noexp' case!

02 February 2014 978 2 View

How can you find the ancestors of a bacterial species?

I would like to demonstrate that Haemophilus influenzae, a common human pathogen, lacks numerous genes in comparison with its ancestor due to genome reduction. I need to know its ancestor to...

02 February 2014 8,937 2 View

What do you think about this correlation between qPCR and RNA-seq?

I would like to know your opinions about the correlation I obtained between qPCR and RNA-seq for 8 genes, two of them being reference genes. The r2 is good but I worry that qPCR FC are not as high...

01 January 2014 7,922 17 View

What is the minimum RNA quantity for a 20 uL RT-qPCR ΔCt-method?

Hi, I would like to know the cDNA quantity you recommend for the mentioned PCR. It will be used to validate RNA-Seq results. Thanks, Bernardo

01 January 2014 8,100 9 View

Can anybody provide me with a list of all reported bacteria, including their corresponding phylum, class, order, and family?

Basically, I'm looking for the same table than this one (http://genomesonline.org/documents/Export/gold.xls) and this one from GOLD genomes (http://genomesonline.org/cgi-bin/GOLD/index.cgi), but...

12 December 2013 10,002 5 View

RT-qPCR of selected differential expressed genes: which dilutions in calibration curve?

I've seen in MIQE guidelines that calibration curves a needed when performing RT-qPCR. I'll use genomic DNA to perform these calibration curves. My question is that I don't know the range of...

12 December 2013 293 3 View

How to get conservation of vaccine candidates between hundreds of bacterial strains?

Hi community, We have identified vaccine candidates via an ex-vivo RNA-seq approach. The next step would be to perform conservation of these candidates (about 20) between multiple bacterial...

12 December 2013 9,574 1 View