User: bioPiraten

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bioPiraten10
Reputation:
10
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New User
Location:
Denmark
Last seen:
1 year, 6 months ago
Joined:
2 years, 6 months ago
Email:
j*********@gmail.com

Posts by bioPiraten

<prev • 6 results • page 1 of 1 • next >
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Comment: C: map proteins to EC numbers (KEGG)
... I guess this is one option, but it is not as clean as going directly to KEGG. If it is not possible to download KEGG directly then I might have to go to a solution like this ...
written 23 months ago by bioPiraten10
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Comment: C: map proteins to EC numbers (KEGG)
... These are non-yeast species and have not been sequenced before, so I guess this methods does not work. ...
written 23 months ago by bioPiraten10
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map proteins to EC numbers (KEGG) in non-model fungal organisms
... Hi All, I have multiple annotated fungal genomes and I would like to map their proteomes to KEGG and infer EC number information for all of them. My idea is to download the KEGG db (or at least the last free version from 2012) and construct an HMM using hmmer for each EC number, which I can then u ...
kegg hmmer written 23 months ago by bioPiraten10 • updated 23 months ago by Manuel Landesfeind1.1k
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Comment: C: Not getting all hits in blast+ all. vs. all
... Thanks, I will try that. I am analysing a specific protein domain, which I have extracted from 30 organisms and now I want to look at the similarity distribution, and infer phylogenetic relationships. I figured blast was the most feasible way of getting % identity for all vs. all of 529 sequences wi ...
written 2.3 years ago by bioPiraten10
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Not getting all hits in blast+ all. vs. all
... I realize there are multiple threads and extensive documentation about blast+, but after traversing most of that information, I haven’t been able to find the answer to my problem. I am making an all vs. all blast+ search on private makedb database. I got 529 proteins in my DB, which I make by: m ...
blast+ written 2.3 years ago by bioPiraten10 • updated 2.3 years ago by Michael Dondrup43k
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Getting genbank annotation file from JGI
... Hi All, I would like to extract the genbank or (embl) annotation file from genomes sequenced at JGI, which should serve as input for another tool in my analysis pipeline. At JGI you can download the annotation of the genomes in gff format, and you can get the genome or CDS in fasta format. So my   ...
jgi annotation gff genbank written 2.5 years ago by bioPiraten10 • updated 2.2 years ago by glarue0

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