Questions tagged [virus]
Biological kingdom of 'microparasite' that is unable to replicate without hijacking the hosts replication machinery
7
questions
1
vote
1answer
20 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 ...
2
votes
1answer
38 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/
&...
4
votes
1answer
107 views
What origins for virus HIV1?
What origins for virus 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
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0
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1answer
54 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 (...
0
votes
2answers
194 views
How to get transcriptome FASTA file for viruses for Kallisto pseudo-alignment?
I guess the title is self-explanatory. I'd like to find the reference transcriptome files for a few human viruses. My RNA-seq samples are from human tumor cells that were infected with viruses. The ...
0
votes
1answer
127 views
How to calculate mutation rate and mutation sites in a genome using FASTA file?
I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format.
How I can identify mutations and mutation sites in those genomes using FASTA sequences but how I can do ...
1
vote
0answers
45 views
Alternatives to phrap for merging contigs with overlapping ends?
I have bins from metagenomes generated with metabat2 on bitbucket/berkleylab/scr which are predicted as viral by MARVEL. MARVEL ...
