Bernardo Bello Ortí

11 Questions 6 Answers 0 Followers

Questions related from Bernardo Bello Ortí

Is viral protein expression important for peptide vaccines?

I would like to know if proteins expressed in higher quantities, such as DNA polymerase, would be better vaccine candidates for a T-cell based vaccine. Thanks, Bernardo

24 October 2014 9,230 6 View

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...

31 March 2014 5,339 2 View

For RNAseq enrichment analysis what are some Gene Ontology (GO) alternatives?

I've been able to perform GO enrichment but since 40% of the bacterial genome I'm working has no GO term assigned, its possible I'm loosing important results. I'm looking for alternatives: I've...

25 March 2014 1,698 1 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?

04 March 2014 7,753 5 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...

25 February 2014 4,825 2 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?

16 February 2014 4,290 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!

06 February 2014 9,171 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...

25 January 2014 7,362 16 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

13 January 2014 2,849 11 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...

16 December 2013 3,288 4 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...

04 December 2013 289 3 View