28 Questions 338 Answers 0 Followers
Questions related from Francisco J. Enguita
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...
12 December 2019 7,121 3 View
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...
04 April 2019 8,821 3 View
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
10 October 2018 9,473 5 View
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...
07 July 2018 7,629 1 View
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...
06 June 2018 7,596 3 View
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...
06 June 2018 9,008 9 View
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...
02 February 2018 2,090 16 View
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...
12 December 2017 8,919 12 View
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?....
10 October 2017 8,516 4 View
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...
09 September 2016 1,943 3 View
Dear All I have several MD trajectories generated by NAMD using coarse-grained dynamics. I would like to perform a deep analysis of the data. Is there any specific tool for this kind of...
02 February 2016 4,853 7 View
Looking for contributors in the area of microbial metabolism and synthetic biology for a research topic in Frontiers in Microbiology. Be free to share with your colleagues and...
01 January 2015 3,724 4 View
Dear ALL Do you know any alternative to the TreeDomViewer software to build a phylogenetic tree of a list of protein sequences based on their domain structures? The software should produce protein...
11 November 2014 9,437 5 View
Dear All I am looking desperately for an application to analyze mouse exome data from NGS experiments. I tried SnpEff, but I was not very happy with the results. Any recommendation? Thanks in...
09 September 2014 7,014 13 View
I would like to calculate a Spearman correlation of gene expression using a big dataset containing around 15000 genes, to generate a figure with the correlation coefficients distribution (as...
06 June 2014 7,723 6 View
We are struggling in getting recombination for baculovirus production in E.coli BAC10 cells. Is there any protocol to make "good" competent cells from BAC10 bacteria? Have some of you experienced...
04 April 2014 10,088 1 View
I have some data generated with snpEff, but I would like to represent it in a graphical manner to get an overview of the SNPs happening in all my samples at the same time. Is there any software to...
03 March 2014 1,224 0 View
I got a triangular correlation expression matrix. I would like to know any easy to use software to extract clustering information from this matrix.
03 March 2014 5,833 4 View
I am looking for a relatively user-friendly pipeline for differential expression analysis of miRNAs in illumina data. I have tried miRanalyzer and iMir but I was not able to set up the software in...
01 January 2014 9,912 11 View
I constructed a tree with 30000 different sequences using MAFFT software. After that I applied the cluster algorithm implemented in MCL (http://micans.org/mcl/) and obtained a file with the...
11 November 2013 619 9 View
I produced a phylo-tree with Mafft that contains 30000 nodes. I would like to cluster the nodes to find relevant groups among my genes. I do not have the alignment since Mafft is not able to...
11 November 2013 4,416 12 View
I was wondering if some of you have experience with pL4440 vector for the in vitro production of dsRNA by using T7 RNA polymerase. How is the vector working when compared with the in vivo protocol...
10 October 2013 4,470 3 View
Do you know any software to perform a blind clustering analysis on microarray expression data?
09 September 2013 460 7 View
I would like to know if there is any research network or consortium grouping different labs, and focused on non-coding RNAs, either in Europe or the US.
06 June 2013 560 1 View
The version 2.0 of the miRNAtools webpage is released in a beta version for testing. This page is a compilation of tools to analyze miRNAs and their regulatory actions, that tries to collect and...
06 June 2013 3,157 1 View
Any advice on a free software for processing and data analysis of low-density qPCR-based arrays? I have used Genex, but unfortunately you have to pay after 30 days of a trial.
01 January 2013 6,337 1 View
All we know is that when we increase the levels of a miRNA we expect a decrease of the protein and eventually the mRNA levels of its cognate target. But, what happens to the levels of a miRNA when...
11 November 2012 9,010 5 View
Fractal models described the universe as a chaotic system. Biology also can be explained by using these models in some extend. However I was wondering if some among us have experience in...
09 September 2012 4,147 10 View
