User: Trombone Engineer
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Posts by Trombone Engineer
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... As an easier alternative, you can try using the db2db conversion tool at https://biodbnet-abcc.ncifcrf.gov/db/db2db.php. It has many options to convert to and from, including your goal items of Ensemble ID and gene names. ...
written 12 weeks ago by
Trombone Engineer • 0
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... I am working with Oxford Nanopore Minion data for small genomes that I am trying to assemble with de novo assembly tools. For training, I have a few datasets with reference genomes and have been comparing various de novo assembly tools. So far I have the best performance from Unicycler, but have not ...
written 12 weeks ago by
Trombone Engineer • 0
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12 weeks ago by
Mensur Dlakic • 9.1k
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... Thank you. What would be a good tool recommendation to determine which genes are shared between all bacteria, then bacteria and archaea? Basically a MSA tool? Are there tools designed for metagenomes that get shotgun sequenced? ...
written 6 months ago by
Trombone Engineer • 0
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... Not an evolutionary biologist, but thought someone here might have insights. A Google search mostly returns "the oldest bacterial genome/DNA we have recovered." However, my question is which bacterial genes evolved earliest, and are thus the oldest?
The idea came from a past project I worked on, in ...
written 6 months ago by
Trombone Engineer • 0
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... What technique does proteomic software use to predict if separate sequences originate from the same protein?
In some of the proteomics data I have worked with, preprocessing steps included the ability to differentiate peptides representing unique proteins, from (multiple) peptides coming from the s ...
written 8 months ago by
Trombone Engineer • 0
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Comment:
C: How to map taxonomy to OTUs
... What IDs are your OTUs? If you are using Green Genes, you can look at the precalculated file for your percent similarity (i.e. 97%) and see the complete list of IDs and taxonomy. Are you using QIIME to use assign_taxonomy.py or is there a reason you are using a different method? Local blast can be h ...
written 3.2 years ago by
Trombone Engineer • 0
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... What Computational Tools Specialize in Human Cell Types? I do a fair amount of genomic and metagenomic analysis on microbiome datasets as well as human data and conclusions from other studies. What computational tools exist that can specialize in genomic inference specific to a single type of human ...
written 3.6 years ago by
Trombone Engineer • 0
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3.6 years ago by
Samuel Brady • 320
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... For anyone who might look this up, I did actually find this information within KEGG's website. The URL http://www.genome.jp/kegg-bin/get_htext?br08201.keg, which is available from the webpage http://www.genome.jp/kegg/brite.html and listed on the link for "Enzymatic reactions" shows all of the react ...
written 3.6 years ago by
Trombone Engineer • 0
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... For software that I have been installing and trying to use, I often see dependencies that require a certain version of software that is not the most current version. How reasonable is it to install multiple versions of software so that I have the most recent version, in addition to an older version ...
written 3.9 years ago by
Trombone Engineer • 0
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3.9 years ago by
h.mon ♦ 32k
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... I would like to assemble a network connecting some genomic data based on metabolism and KEGG reaction IDs. Is there a way that I can view all reactions listed on the KEGG database? ...
written 4.0 years ago by
Trombone Engineer • 0
• updated
3.6 years ago by
EagleEye ♦ 6.8k
Latest awards to Trombone Engineer
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created a question with more than 1,000 views.
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created a question with more than 1,000 views.
For How to install multiple software versions on the same computer?
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