Questions tagged [virus]
Biological kingdom of 'microparasite' that is unable to replicate without hijacking the hosts replication machinery
31
questions
0
votes
0
answers
19
views
Estimating rate of evolution from a phylogeny
Any suggestions for the best way to estimate a metric for evolutionary rate of viral sequences of the same species?
I was using terminal branch length from a phylogeny and would quite like to try sub ...
1
vote
1
answer
70
views
Choosing the best number of species for assay
I am doing amplicon sequencing of a virus across many different regions. Lets say I have 20k unique variants of the same virus that I put into my pcr assay and after sequencing and amplifications I am ...
- 121
3
votes
1
answer
109
views
What is the limit of partition incompleteness in Bayesian MCMC?
I am seeking advice on whether or not to incorporate incomplete data into my BEAST analysis.
I have HIV data consisting of two partitions of the pol gene: one that is 1.2 kb in length and present in ...
- 435
1
vote
0
answers
15
views
DNASTAR viral-host integration assembly keeps failing
I have two NGS files from an NGS company corresponding to the sequencing data from a tumor sample as follows:
TB_7710391_R1.FASTQ.gz
TB_7710391_R2.FASTQ.gz
I have downloaded the genome for MCPyV as ...
1
vote
2
answers
87
views
How can I detect MCPyV in a FASTQ file?
I have received two NGS files from an NGS company, both are FASTQ files that correspond to reads from a tumor sample. I heavily suspect that MCPyV is present, and I am hoping to identify it.
What ...
4
votes
2
answers
181
views
relation between Illumina sequencing primer and viral sequences
Dealing whith a problematic sequencing run I found this over-represented sequence:
GGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGGCGTCTTCTGCTTG
It is clearly relate to the Illumina sequencing primer ...
- 333
1
vote
1
answer
100
views
Is current AI able to generate RNA sequences of viruses? [closed]
After seeing a video of a combination of CRISPR and AI, and an article of someone who made two babies immune against HIV and still healthy, I wondered about something. If such complicated thing, to ...
- 13
3
votes
1
answer
66
views
Metagenomics pipeline recommendations for short-read data
de novo metagenomics on viral NGS data is a hot-topic. On this site alone at least 4 specific algorithms have been used to identify multi-strain/multi-species for a given data set, however these do ...
M__♦
- 12.8k
-1
votes
2
answers
57
views
How to use GEO_SPHERE?
I have some problems with geosphere package which extends/applies the Beast Bayesian MCMC package for calculating phylogenetic trees. Please, could anyone give any hints about at least one of them?
...
- 435
3
votes
2
answers
170
views
How to get the number of complete phage genomes available on ncbi?
I am looking to establish the total number of complete phage genomes available on NCBI.
I am not looking for any specific type, but want to understand the total diversity available.
How can I perform ...
2
votes
1
answer
58
views
Demovir produces an empty output
I am new to bioinformatics and am working on viral metagenomic (virome) datasets and so would like to use Demovir* for doing taxonomic annotations on my viral contigs.
First, I installed all ...
- 41
2
votes
1
answer
576
views
Entrez (Biopython) esearch and efetch not returning sequence as expected
I'm trying to use Entrez (through Biopython) to download the sequence of a TMV replicase gene.
I have the following code:
...
- 23
3
votes
2
answers
89
views
Gold standard benchmark
This page is claimed to contain a gold standard benchmark for viral genome assembly.
https://github.com/cbg-ethz/5-virus-mix
The claim is here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/
...
- 359
3
votes
1
answer
140
views
What is the origin of HIV1?
What is the origin of HIV1?
This is the alignment of a small part of the POL protein of the HIV1 virus GenBank KU749412.1, with the POL protein of the Visna virus GenBank L06906.1
...
- 215
1
vote
1
answer
67
views
Align the HIV-1 Gag protein with the Gag protein of Visna virus
Align the HIV-1 Gag protein with the Gag protein of Visna virus
Background Visna virus is a lentivirus causing encephalitis in sheep
The problem is align the follow two protein Gag of viruses HIV-1 (...
- 215