Are there alternatives to TreeDomViewer software?

More Francisco J. Enguita's questions See All

Do you have a template for miRNA qPCR arrays from Qiagen (former Exiqon)?

Dear colleagues After a lot of struggle with the new rebranding of Exiqon that sold the LNA technology to Qiagen, we decided to give a try to the new miRNA qPCR arrays. We bought the whole...

11 December 2019 7,166 3 View

How to refine a protein-drug complex structure coordinates?

I have a protein-drug complex obtained by virtual drug screening. How can I refine the coordinates of the whole complex?. Is energy minimization the best protocol to be applied? Thanks in...

03 April 2019 8,863 3 View

RNAse R... which supplier?

Dear All I am looking forward to treat my total RNA samples with RNAse R. Any suggestions about which supplier do you prefer for purchasing it?. Thanks. Best

09 October 2018 9,518 5 View

How to over-express a selected circular RNA?

Dear All Do you have experience in methods for the over-expression of selected circular RNAs in human or mouse cells?... If yes... which strategy did you use?... which vectors and...

06 July 2018 7,681 1 View

What is your favourite Gene-enrichment analysis in a graphical environment?

Hi there I would like to know and to get your feedback about you favourite Gene-enrichment analysis software based in a graphical environment, preferably on-line. Please give me your feedback...

05 June 2018 9,060 9 View

How is the performance of Nanostring system to detect extracellular miRNAs?

Dear All I wanted to give a try to Nanostring system to detect extracellular miRNAs in a screening-based approach. I am wondering if some of you have experience with Nanostring in the detection...

05 June 2018 7,635 3 View

Someone has experience with the new Exiqon-Qiagen miRNAnome qPCR screening panels?

Dear All I had used for a while the Exiqon miRNAnome panels based on low density qPCR arrays. However, since the begginning of this 2018, Exiqon has joined Qiagen. I ordered the same screenings...

01 February 2018 2,140 16 View

How to compare two XPM contact matrices generated by GROMACS?

Hi there I got several contact matrices in XPM format generated by GROMACS trajectories for a series of protein mutants. How to compare them to extract the differences between atom contacts in...

11 December 2017 8,959 12 View

Any web-based tool to get statistics about location and miRNA expression?

Hi there I am dealing with a long list of miRNAs... I would like to get some tool to organize them by functional groups, clusters, chromosome location, tissue expression, etc... Any suggestion?....

09 October 2017 8,554 4 View

Is there any alternative to Green A Dyematrex gel (Amicon) for pseudo-affinity chromatography?

I am trying to reproduce an old purification protocol from 2004 that claims the use of a pseudo-affinity chromatography based on Green A Dyematrex gel (Amicon). The product is discontinued from...

08 September 2016 1,990 3 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 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

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 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

Transfection in HEK293T cells?

Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...

31 July 2024 9,892 4 View

How to retain the a GFP tagged gene expression in stable cell line?

Hello , I established a stable cell line expressing GFP tagged to a centrosomal gene having G418 drug selection marker. I validated the stable line by IFA and Western blotting, results are fine....

29 July 2024 5,007 0 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 View

Sunil S Adav

Try Mega (Molecular Evolutionary Genetics Analysis) or Bioedit.

Rene Mulder

Dear Paco,

I believe that you can ask Romain Studer for suggestion. He and I have recently published work using phylogenetic analysis. I think he can help.

Could luck.

René

Andrea Masotti

Yes, maybe MEGA5 should work.

Cheers, Andrea

Francisco J. Enguita

Thanks my friends !... I will try your suggestions...

Mohamed Mohsen Gammoudi

Please, read this paper. I hope it helps you.

http://www.kenbenoit.net/courses/tcd2014qta/readings/Jivani_ijcta2011020632.pdf

Best regards.