26 Questions 33 Answers 0 Followers
Questions related from Guillermo Domínguez Huerta
Do you know any database for protistan viruses? Thank you!
07 June 2022 1,831 0 View
I have a cloud plot of data relating two important variables for an ecological analysis. I was defining the "abnormal class" as the data points that are >=20 for the Y-axis and >=20 for the...
23 September 2020 7,921 16 View
Hi all, I am finding proteins that might be made with ribosomal frameshiting. When I get the protein using Transeq for the 6 frames, I got two translations from frames +1 and +2 that had a match...
18 May 2020 2,683 0 View
Hi all, I have a collection of nucleotide sequences corresponding to one functional domain of a hallmark gene of viruses. So in principle I am working with relatively-homogeneous functional...
29 March 2020 9,128 3 View
Hi all, I am looking for a way to find RNA virus genome termini in metatranscriptomes. Do you know a database of sequences for RNA virus genome termini? Or if they are certain motifs repeated...
10 November 2019 549 2 View
Hi all, We are looking for active infection of RNA viruses in metatranscriptomes of complex environmental communities. What sequences would you use to find active retroviral infections? When...
24 October 2019 3,232 0 View
Hi all, I am wondering how one should define OTUs from metagenomic/metatranscriptomic datasets. I guess protein identity (instead of nucleotide identity) should be used given the higher...
23 August 2019 3,212 6 View
Hi all, I'm working to extract RNA virus sequences from metatranscriptomic datasets. I observed that it is possible to detect some "virus" signal from non-assembled reads (by translation and...
03 June 2019 5,963 1 View
Hi, I'd like to know what difference makes using FULL PROTEIN SEQUENCES versus PROTEIN CONSERVED DOMAIN SEQUENCES in order to make a phylogenetic tree. In my case, the goal is to put in...
24 April 2019 3,308 4 View
Hi all, I was performing TRIzol extraction protocol to get prokaryotic RNA. Samples were treated with rigorous Turbo DNase treatment. Results were good in terms of quantity (50-100 ng/ul)....
06 February 2019 7,047 2 View
Hi all, I'm looking for the expert opinion from a chemist, since I am only a biologist. I have a set of samples made in the following manner: many litters of seawater were...
04 August 2018 4,157 3 View
Hi all, this one is a (I guess) tricky question... RNA virus discovery from metagenome/metatranscriptome dataset (overall from environmental samples) is particularly difficult because of their...
23 July 2018 4,469 1 View
Hi all, I'm trying to get proteins predicted from novel eukaryotic DNA sequences obtained from metagenomics. I guess protein prediction can be problematic from eukaryotic genomes.... WHAT ARE...
29 May 2018 7,889 4 View
Hi all, I would like to compare (using blastx) a set of assembled contigs against the database of all reference RNA virus proteins within the taxonomic classes ssRNA viruses (txid 439488), dsRNA...
25 May 2018 3,620 4 View
Hi all, I'm trying to purify viral RNA from water samples precipitated with ferric chloride. We are putting a dsRNA and a ssRNA virus isolates in a volume of buffer optimal for the virions....
30 March 2018 6,596 2 View
Hi all, I wondering about bioinformatic tools to capture "RNA viruses" from environmental sequence datasets. dsDNA phages are pretty abundant and have relatively conserved hallmark genes....
05 March 2018 4,123 5 View
I want to precipitate a cystovirus, which is en enveloped phage. Any of you know if this kind of viruses should be subjected to different conditions when you precipitate with PEG? I mean: PEG and...
27 January 2018 6,264 1 View
Hi all, I looking for literature evidence for this phenomenon. Apparently, RNA (I'm not sure if also DNA) is cleavaged in a non-enzymatic manner by iron. I would need some theory to support...
20 January 2018 3,243 4 View
Hi all, I know this is a typical phenomenon, but after reading I'm not getting a convincing explanation. I prepared 4 L of a buffer containing 10 mM KH2PO4 and 1 mM MgSO4*7H2O. This time I...
12 January 2018 959 6 View
Beyond human pathogenic viruses (enteroviruses, hepatitis A virus, rotavirus, norovirus)..., which other riboviruses are expected to found in freshwaters from an urban river? I'm looking for...
18 December 2017 7,345 2 View
Get rid of the iron from my samples. Iron chelating capacity of EDTA? Briefly, I have samples consisting of resuspended viruses precipitated with FeCl3. After flocculation of viruses, I resuspend...
11 December 2017 6,916 7 View
I have to get rid of dsRNA in a sample of the phage Phi6, whose genome is dsRNA. Ribonuclease A (bovine pancreatic) doesn't look like it's working very well for this goal, at least incubating at...
09 November 2017 4,867 2 View
Hi, If you want to get RNA genomes from viral capsids and get rid of the free nucleic acids ... do think RNases can significantly affect the RNA inside the capsids? Also, what method to...
08 October 2017 9,637 4 View
Hi, I have some data to do statistcal analysis. They are mutation frequency of different ORFs, but some of the frequencies are 0. Which test would you use to observe differences? chi-square test,...
22 June 2017 568 8 View
Hi, Imagine you got a mutant library of a plasmid DNA generated by random mutagenesis and affecting the whole plasmid sequence. This mutant library is going to be used to transform bacteria and...
29 May 2017 4,724 5 View
Hi, I got a random mutation library of a plasmid DNA generated by error-prone amplification. How do I know that my mutant library has a wide variety of changes? which are the (statistical)...
29 May 2017 415 8 View
