User: SilentGene

gravatar for SilentGene
SilentGene30
Reputation:
30
Status:
New User
Location:
The University of Melbourne
Last seen:
2 months, 2 weeks ago
Joined:
4 years, 7 months ago
Email:
l**********@gmail.com

Posts by SilentGene

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Genome annotation to KEGG KO ids
... As an alternative solution, you can annotate your genome using [Prokka][1], and then use [this script][2] to convert the result from Prokka to the KEGG annotation. You can do this on your local laptop efficiently instead of uploading your genomes to other web servers such as `blastkoala`. [1]: h ...
written 9 months ago by SilentGene30
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Answer: A: taxonomic assignment of metagenomic bins and detect 16S rRNA gene in metagenomic
... Hi there, apart from using `blastn` against nr databases to assign taxonomy of the metagenomic bins. I recommend you to try out the following 2 software: 1. `phylophlan`. This software could help you integrate metagenomic bins in the 'tree of life' which has already involved over 3000 microbial gen ...
written 13 months ago by SilentGene30
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Answer: A: How To Remove The Same Sequences In The Fasta Files?
... Try to use [this][1] python script, which can help you remove duplicates of the sequences in one or several fasta files. And it's easy to use `--id` or `--seq` option to indicate whether you like the filter to work according to the id or the sequence itself. [1]: https://github.com/SilentGene/Bi ...
written 14 months ago by SilentGene30
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Answer: A: python blast to mcl
... Hi, I think you may want to try this [POCP-matrix][1] script. It can calculate the POCP value between two or more genomes, and all you need is simply to have BLAST+ and python3 installed. [1]: https://github.com/SilentGene/Bio-py/tree/master/POCP-matrix ...
written 14 months ago by SilentGene30
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Answer: A: Glimmer 3 multi-extract input problem
... hi, have you solved this problem? I met the same problem as yours. What do you do next? ...
written 4.6 years ago by SilentGene30
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glimmer ERROR: Skipped following coord line
... when I use glimmer to predict ORF in genomes, there is an error occurred: Optimizing... Step 7 of 8: Getting start-codon usage ERROR: Skipped following coord line >2 ERROR: Skipped following coord line >3 ERROR: Skipped following coord line >4 Step 8 of 8: Running second Glimmer3 Pl ...
genome glimmer written 4.6 years ago by SilentGene30
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glimmer: Error parsing .upstream file. "Not a Fasta file?"
... When I use glimmer3.02 to predict orf, there is an error occurred. The script I used is g3-iterated.csh. The error is: Step 5 of 8: Getting training coordinates Step 6 of 8: Making PWM from upstream regions Segmentation fault (core dumped) Error parsing file 'out.glimmer.upstream'. Not a Fasta ...
software error genome written 4.6 years ago by SilentGene30

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For glimmer ERROR: Skipped following coord line
Popular Question 2.4 years ago, created a question with more than 1,000 views. For glimmer: Error parsing .upstream file. "Not a Fasta file?"

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