How can I identify pseudogenes in prokaryotic genomes?

More Bernardo Bello Ortí's questions See All

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...

02 March 2014 4,167 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?

02 March 2014 2,026 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...

01 February 2014 8,880 2 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...

01 February 2014 6,591 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!

01 February 2014 921 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...

01 February 2014 4,245 10 View

No title

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

31 December 2013 8,033 9 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...

31 December 2013 7,858 17 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...

11 December 2013 9,942 5 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...

11 December 2013 9,522 1 View

How to normalise data on OPM package from R Studio ?

Good afternoon, I recently used OmniLog from BIOLOG for my experimentations : I tested the metabolism of different strains on 2 types of plates. I have 16 strains of 3 different groups...

02 March 2021 3,584 1 View

What is the exact mechanism of the antimicrobial effect of local anesthetics?

The antimicrobial effect of local anesthetics has been known for more than 50 years, but it still seems to have an unclear mechanism of action. which bacteria? which concentration? etc etc. ....

27 February 2021 4,450 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Is there any one who can provide a donation of HPV detection and genotyping kits in exchange collaboration fors?

Warm greetings My name is Ayichew S. and I am doing my Ph.D. in Medical Microbiology (on Human papillomavirus). At this stage, I have almost completed a clinical sample Cervical swabs)...

25 February 2021 1,660 3 View

Is there any one who can provide a donation of HPV detection and genotyping kits in exchange collaboration forms?

Warm greetings! My name is Ayichew S. and I am doing my Ph.D. in Medical Microbiology focusing on Human papillomavirus). At this stage, I have almost completed a clinical sample (Cervical swabs)...

25 February 2021 3,612 3 View

Uncertianiny in using dry or wet basis in mixing a sediment with fuel oil?

Hello I'm currently working on a topic related to studying the anaerobic biodegradation of TPH in marine sediments. In this work, sediment should be mixed with fuel oil to a concentration of 20 g...

24 February 2021 9,839 3 View

Advice on growing lactobacillus species in the lab?

Hello everyone, For part of my PhD project, I'm hoping to grow some lactobacillus species in the lab so that I can create standard curves for a qPCR quantification of a faecal sample. However, I...

24 February 2021 3,157 6 View

What are the best cations for preparing competent cells, Ca2+ or Mg2+?

I have been reading various articles and most state that treatment with CaCl2 produces higher efficiency of transformation than MgCl2. Can anyone explain why Ca2+ is better than Mg2+ at...

16 February 2021 8,519 5 View

How to consider effects of rapid warm adaptation in modeling of ecological impacts of warming?

I would highly appreciate it if my fellow ecologists (biologists) provide their opinion on the thoughts below [esp., shortly tell us which path may be more effective, if they know another way, if...

15 February 2021 3,642 6 View

Differences between sheep blood with Alsever solution vs citrated/defibrinated sheep blood in microbiological media?

I am aware of a study that has compared the use of citrated and defibrinated sheep's blood in microbiological media (Hair Sheep Blood, Citrated or Defibrinated, Fulfills All Req... ), but can...

10 February 2021 5,927 1 View

Christian Rückert

You might try the approach the NCBI uses in the PGAP pipeline: BLAST all proteins against a central database. If two adjacent proteins hit one larger protein in the database, this pair is flagged for closer inspection.

From my experience, this usually results in 10 to 20 candidate pairs in a 3 Mbp genome.

Jeremy Chase Crawford

Many people say they exclude psuedogenes from their data sets by looking for nonsense codons and stop codons in their sequences. I don't think that's the best way, but it's certainly something people have been doing for a while now.