User: Optimist

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Optimist100
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Posts by Optimist

<prev • 61 results • page 1 of 7 • next >
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Comment: C: Prokka Annotation or NCBI Annotation
... 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 Optimist100
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Answer: A: Selection of Multiple Sequence Alignment Tool
... 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 Optimist100
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Should we remove plasmid sequences for Whole genome Alignment
... 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 ...
genome alignment plasmids written 9 days ago by Optimist100
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Comment: C: Prokka Annotation or NCBI Annotation
... 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 Optimist100
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Prokka Annotation or NCBI Annotation
... 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 ...
ncbi prokka genbank written 11 days ago by Optimist100 • updated 11 days ago by Mensur Dlakic7.1k
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Tools for Whole genome phylogeny
... 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 ...
phyogeny bacterial genomics written 23 days ago by Optimist100
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Comment: C: extract a DNA sequence based on header in multifasta file
... Thanks for the trick. awk has worked for me. ...
written 27 days ago by Optimist100
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extract a DNA sequence based on header in multifasta file
... Hello all, My multifasta file with rRNA sequences looks like this. >16S_rRNA::1:4-522(-) TGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGCGTGATGGCGGGAACTCAAAGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAG ...
fasta sequence extraction written 27 days ago by Optimist100 • updated 27 days ago by shenwei3565.6k
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How to generate WGS Multiple sequence alignment file
... 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 ...
multiple sequence alignment written 28 days ago by Optimist100
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(Closed) Certificate verification failed: SecurityAppliance_SSL_CA
... 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:/ ...
certificate verification sophos written 4 weeks ago by Optimist100

Latest awards to Optimist

Popular Question 5 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 6 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 6 months ago, created a question with more than 1,000 views. For Finding of origin of replication in a bacterial Genome
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Intall local BLAST in Ubuntu
Popular Question 13 months ago, created a question with more than 1,000 views. For Finding of origin of replication in a bacterial Genome
Popular Question 16 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 17 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Supporter 17 months ago, voted at least 25 times.
Popular Question 22 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
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