User: Optimist
Optimist • 100
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Posts by Optimist
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... Should I modify the command in order for prokka to use the 3 databases? or it takes it automatically??
I have run this 'prokka --setupdb'
This is the command i generally use to run prokka
prokka GCA_000168335.1_ASM16833v1_genomic.fasta --outdir GCA_000168335.1_ASM16833v1_prokka_compliant_out_29-1 ...
written 8 days ago by
Optimist • 100
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... Offline Tool: MEGA - https://www.megasoftware.net/
Online: Galaxy - https://usegalaxy.org [Galaxy has a wide range of tools among this for various analysis.]
...
written 9 days ago by
Optimist • 100
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... Hello there!!
Should we remove plasmid sequences from genome assemblies for Whole Genome alignment?
I want to perform Whole genome alignment among 20 bacterial genomes. of 20, only 5 genomes have plasmids in them while the rest have only chromosome.
Is it advisable to remove those plasmid sequenc ...
written 9 days ago by
Optimist • 100
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... I have just checked my Prokka and It has following databases
Looking for databases in: /home/bio2/miniconda3/envs/prokka_env/db
* Kingdoms: Archaea Bacteria Mitochondria Viruses
* Genera: Enterococcus Escherichia Staphylococcus
* HMMs: HAMAP
* CMs: Archaea Bacteria Viruses
As you rightly pointed ...
written 11 days ago by
Optimist • 100
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... Dear All,
I have two sets of annotation files for 15 Bacterial genomes. One set from NCBI annotations (from RefSeq) and the other from Prokka (I have run it in my local machine).
Which one is advisable to use between the two for all downstream analysis?
Awaiting your valuable feedback
Thank You ...
written 11 days ago by
Optimist • 100
• updated
11 days ago by
Mensur Dlakic • 7.1k
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... Are there any tools that can perform Whole Genome Phylogeny among 100 bacterial genomes and also provide Bootstrap Values.
I tried m hands on RealPhy. But they do not provide bootstrap values.
Can someone please suggest a tool for Whole genome phylogeny that provides bootstrap values too.
Thanks a ...
written 23 days ago by
Optimist • 100
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... Thanks for the trick. awk has worked for me. ...
written 27 days ago by
Optimist • 100
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... Hello all,
My multifasta file with rRNA sequences looks like this.
>16S_rRNA::1:4-522(-)
TGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGCGTGATGGCGGGAACTCAAAGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAG ...
written 27 days ago by
Optimist • 100
• updated
27 days ago by
shenwei356 ♦ 5.6k
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... Can you please help me tools that can be used to generate an alignment file using 16 bacterial whole genome sequences. Size of the genomes varies between 3.8 Mb to 4.2 Mb.
I need the alignment file generated by Multiple Sequence aligner as an input for gubbins tool.
Which tool can be used for achi ...
written 28 days ago by
Optimist • 100
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... Can somone please help me in solving this issue.
Im getting this Certificate verification failed er
Sudo apt-get update
My organisation uses sophos firewall. Will 'SecurityAppliance_SSL_CA.pem' certificate help me solve this??
Hit:1 http://mirror.cse.iitk.ac.in/ubuntu bionic InRelease
Hit:2 http:/ ...
written 4 weeks ago by
Optimist • 100
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