Skip to main content
3 votes

detecting DNA of possible infection on cell line

I've had some success looking for contamination in Illumina and Nanopore reads using kraken2. Kraken2 has a phylogenetic-based approach, which in the first instance tries to find the most specific ...
gringer's user avatar
  • 14.3k
3 votes

1.What size PCR product will be generated using the primers (bold and underlined) in the sequence below?

Without giving too much of the "what they want you to do yourself" bits of this away, here are a few explanations of the image that may help you answer this question: As mentioned in the ...
gringer's user avatar
  • 14.3k
2 votes

What options are there for visualising DNA sequences?

DNA sequences have a massive range in length, so the approach of visualisation is dependent on the purpose of that visualisation. I have been experimenting with visualising the repetitive structure of ...
gringer's user avatar
  • 14.3k
2 votes

How many ML tree should I build?

Simply use the iterations option (e.g. -n 1000) of IQTREE. It's a lot quicker (several logs) and is strongly of identical performance to RAxML. ...
M__'s user avatar
  • 12.6k
1 vote

Is there a database of oligonucleotide duplex sequences and their melting temperatures

Not exactly what you're asking, but the modeling program/API ViennaRNA has excellent and accurate utilities for predicting the stability ($\Delta \Delta G$ of folding) for arbitrary oligonucleotide ...
Maximilian Press's user avatar
1 vote

How to download the same 18S rRNA gene region for multiple species?

I can suggest two ways to batch-download aligned sequences for the species of interest. Both ways are integral to the Ensembl database and toolsets. But before that, I suggest FBgn0085802 (which is ...
44Pasha's user avatar
  • 21
1 vote

How to download the same 18S rRNA gene region for multiple species?

How do I know which sequence I should use to make an alignment with other species? Use both. For fruit flies there should thousands of 18S sequences. How can I batch download the same region for all ...
M__'s user avatar
  • 12.6k
1 vote

Sequence Alignment for sequences with the same length

I see ... the application is if two genes had the same number of indels* at different homologous positions within the gene. This happens but equally one gene might have an indel and another gene might ...
M__'s user avatar
  • 12.6k
1 vote

Seeking Guidance on Designing DNA Sequences with Specific Criteria

It is not difficult to simulate every 10mer DNA oligo, here is some Python code that will do that: (there is probably a more elegant way to do this) ...
Maximilian Press's user avatar
1 vote

detecting DNA of possible infection on cell line

I didn't manage to try the ones reported by @gringer and @alexlok here, but I did manage to perform an analysis using the OneCodex webapp: https://app.onecodex.com/ and based on the experimental ...
719016's user avatar
  • 2,324
1 vote

detecting DNA of possible infection on cell line

Maybe less advanced but worth mentioning, I've had good results with fastq_screen. It's simply trying to align a subset of your sequences against various genomes (comes with a few genomes, you can add ...
Alexlok's user avatar
  • 384

Only top scored, non community-wiki answers of a minimum length are eligible