Can anyone recommend me an universal primer pair for bacterial lipase gene amplification from environmental metagenomic samples?

RAJAL DEBNATH @RAJAL_DEBNATH

12 December 2013 1 670 Report

I am interested in any program for degenerate primer designing other than CODEHOP.

Fabrice Armougom

You can try this tool :

http://bibiserv.techfak.uni-bielefeld.de/genefisher2/

or this one (but you have to download the software and used it locally:

http://acgt.cs.tau.ac.il/hyden/

Web_service here:

http://www.changbioscience.com/primo/primod.html

reccently 2013: in this article :

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600133/

hope it can help you

Fabrice

Badges
Science method

More RAJAL DEBNATH's questions See All

Any thoughts on uncultured microbe isolation?

With the involvement of NGS, most of the researchers have moved to desk than to bench. At bench we understand the biological entity with chemicals and pipettes by monitoring them at specific...

05 June 2015 4,487 11 View

Research in the ERA of OPEN access ??

With open access, you have the liberty of getting more citations because everyone can read it and draw conclusions or relate to their findings, for which a researcher at one end pays the money and...

05 June 2015 8,015 2 View

Can anyone help with the R code for distance decay relationship?

I am required to do distance decay analysis for my NGS bacterial community along a geographical gradient. What metadata fields are required for the gradient. Will the geographical co-ordinates...

04 May 2015 5,337 2 View

Shared phylotype analysis?

Shared phylotype analysis among sites to visualize spatial effect on microbial communities. How is shared phylotype analysis carried out with geographic distance ( I am aware of generating the...

04 May 2015 3,941 1 View

How do I visualize the bacterial genome using the ggbio R package/Circo?

I need help on visualizing a microbial genome sequence obtained from Miseq-paired end reads. I am not sure, when using the tools, how the input file should look. Can anyone help me with generating...

10 November 2014 3,865 3 View

Does anyone have knowledge on the total protein isolation for enzyme characterization?

Hello everyone, I intend to isolate total protein from bacterial cells (in terms of both quality and quantity). My protein is basically an enzyme and hence I will be analyzing its activity. It...

07 August 2014 4,089 1 View

Can anyone help with a lipase primer design from genus Pseudomonas?

I write here to seek help on isolating a lipase gene from a bacterium LTR48. I am trying to amplify lipase from a bacterium which is most likely a Pseudomonas baetica (dendrogram attached). But...

07 August 2014 4,677 3 View

PCR by setting annealing point of primers way below the temperature of melting?

What would you expect if a particular PCR protocol is carried out by setting the annealing temperature of primers at 42 or 45 degree centigrade whereas the actual (calculated) temperature of...

11 December 2013 425 5 View

Blast sequence analysis for 16S rRNA gene

A forward primer sequence for a 16S rRNA gene on BLAST shows identification with Strenotrophomonas maltophilia having the following output for the first four matches:...

04 May 2013 6,763 1 View

Removal of secondary bands from PCR.

Normal amplification of the particular gene with the same set of primers is routine work for me. But this is how it all got ruined. I am amplifying a set of reaction for sequencing but I am...

02 March 2013 6,325 10 View

How to confirm the site-directed mutagenesis result without performing NGS?

I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...

08 August 2024 4,645 2 View

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

Research Methodology - Impact of Corporate Reputation on Stakeholders Behaviors?

Please can anyone support with the survey questions based on RQ measures and propose how to do it in FMCG industry and include as well the role of brand equity Thanks

06 August 2024 949 0 View

How much total RNA concentration to be extracted from sorted plasma cells from bone marrow of C57BL/6 mice for RT-PCR ?

i have sorted anti-NP specific plasma cells from bone marrow of C57BL/6 mice at certain times after immunization with variable counts and isolated total RNA using TRIZOL method for RT-PCR using...

05 August 2024 8,835 1 View

Why after performing site directed mutagenesis ,I don't see any colony after transformation?

I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...

05 August 2024 9,059 3 View

Anyone having idea about VN primer for miRNA primer design ?

How to design VN primer to attach with universal reverse primer

05 August 2024 2,116 3 View

Should I remove an item from a scale to raise Cronbach's alpha and McDonald's omega or is it better to leave it if they are both over .7 already?

Hello! I have this scale which had 10 items initially. I had to remove items 8 and 10 because they correlated negatively with the scale, and then I removed item 9 because Cronbach's alpha and...

01 August 2024 4,606 7 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,079 0 View

I'm optimizing a tetra-ARMS PCR protocol with amplicon sizes: 165bp, 123bp and 93bp. Why, in the gel, only 165bp is visible while I'm expecting all 3?

It's an end-point PCR protocol. I'm using 1.5% agarose gel with SyBR Safe dye and TBE as a running buffer, visualization on BioRad XR+ system. I was primarily thinking of primer efficiency,...

01 August 2024 4,673 4 View

PCR showing no bands - Master mix and primers didn't mix?

Hello everyone, I performed a PCR yesterday, and the results showed no bands on the gel. Of course, I probably missed some crucial steps, like adding my samples to the PCR strips themselves, for...

31 July 2024 2,406 6 View