User: Trombone Engineer

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Posts by Trombone Engineer

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Comment: C: converting Gene Names to ensembl id
... 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 Engineer0
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How to handle multiple contig outputs from de novo assemblers when one contig is desired?
... 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 ...
de novo assembly contig nanopore written 12 weeks ago by Trombone Engineer0 • updated 12 weeks ago by Mensur Dlakic9.1k
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Comment: C: Which bacterial genes are the oldest?
... 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 Engineer0
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Which bacterial genes are the oldest?
... 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 ...
gene bacteria ancient genomics written 6 months ago by Trombone Engineer0
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What technique does proteomic software use to predict if separate sequences originate from the same protein?
... 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 ...
proteomics peptides unique written 8 months ago by Trombone Engineer0
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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 Engineer0
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What Computational Tools Specialize in Human Cell Types?
... 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 ...
genome gene alignment cell type human written 3.6 years ago by Trombone Engineer0 • updated 3.6 years ago by Samuel Brady320
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Answer: A: How to view all KEGG reactions?
... 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 Engineer0
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How to install multiple software versions on the same computer?
... 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 ...
software error written 3.9 years ago by Trombone Engineer0 • updated 3.9 years ago by h.mon32k
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How to view all KEGG reactions?
... 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? ...
genome metabolism reaction koid kegg written 4.0 years ago by Trombone Engineer0 • updated 3.6 years ago by EagleEye6.8k

Latest awards to Trombone Engineer

Popular Question 9 weeks ago, created a question with more than 1,000 views. For How to view all KEGG reactions?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to view all KEGG reactions?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to install multiple software versions on the same computer?

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