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User: Nari

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Nari • 880
Reputation:
880
Status:
Trusted
Location:
United States
Twitter:
BloodTypo
Last seen:
7 months ago
Joined:
8 years, 2 months ago
Email:
n**********@gmail.com

PhD Student interested in Human Microbiome, NGS.

Posts by Nari

<prev • 180 results • page 1 of 18 • next >
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Answer: A: calculating abundance of metagenomes
... https://github.com/HRGV/phyloFlash[phyloFlash][1] which uses SSU 16S against SILVA db. [1]: https://github.com/HRGV/phyloFlash ...
written 7 months ago by Nari • 880
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Answer: A: BPGA cause problem during running
... Mind that **usearch.exe** is not actually **usearch.exe.exe** Quickly check this from file properties. ...
written 2.6 years ago by Nari • 880
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Comment: C: BPGA - Bacterial Pan Genome Analysis pipeline
... COG is 2003 database with update on 2014. As of my knowledge it has not been updated since. So BPGA uses this only. You can use [KAAS][1] to re-annotate the fasta file. [1]: https://www.genome.jp/tools/kaas/ ...
written 2.6 years ago by Nari • 880
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Comment: C: comparison between two orthologs
... Fine, but it would be better if you share the sequences or accession IDs or any kind of results you got after ortholog prediction in your question. ...
written 3.0 years ago by Nari • 880
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Answer: A: comparison between two orthologs
... There always comes a result showing some score (bit score in case of blast based results), to decide which one is the best possible ortholog among the two. Try to find out the "score" or similar parameter to decide best from your results. As OrthoDB uses Smith Waterman algorithm along with CD-HIT yo ...
written 3.0 years ago by Nari • 880
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Comment: C: comparison between two orthologs
... mention which tool you used for ortholog prediction ...
written 3.0 years ago by Nari • 880
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Forum: What are the advantages of purchsing KEGG FTP access over public resources?
... Hello, Our lab can manage to purchase KEGG ftp access for 1 year. We mostly work on microbial genomics and metagenomics. I wonder what would be the added benefit of investing in this. What are the features that [public resource of KEGG][1] do not provide? [1]: http://www.kegg.jp/ ...
gene forum sequence written 3.1 years ago by Nari • 880
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Comment: C: What is unique identifier for organism in NCBI gbff file?
... Thanks for your insights. I just wanted uniqueness within a gbff file (all chr.s and plasmids). And not common for different strain of desired organism. The different assembly version of same strain may not be a problem, as I will find orthologous clusters. What would you suggest considering this. ...
written 3.1 years ago by Nari • 880
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Answer: A: Memory-Efficient Way To Transpose Csv/Text File?
... Try simple perl script here : https://github.com/9aren/Transpose_Matrix/blob/master/Transpose_tsv.pl (No idea if it is memory efficient or not) ...
written 3.1 years ago by Nari • 880
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What is unique identifier for organism in NCBI gbff file?
... Dear all, Wish you a Happy new year 2018. I am trying to parse NCBI gbff files for genomes from NCBI. I am especially interested in coding sequences from one organism at a time irrespective of the plasmid or multiple chromosomes, with a single standard Identifier in CDS fasta headers. As refseq acc ...
genome sequence written 3.1 years ago by Nari • 880 • updated 3.1 years ago by Michael Dondrup ♦ 48k

Latest awards to Nari

Popular Question 19 months ago, created a question with more than 1,000 views. For Where should this tool be published?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How Can I Download Or Get A Pathway List From Kegg
Popular Question 19 months ago, created a question with more than 1,000 views. For Sample ORTHOMCL run on my Fasta file.
Epic Question 19 months ago, created a question with more than 10,000 views. For How To Decide Best Docking Conformation From Autodock Results?
Popular Question 19 months ago, created a question with more than 1,000 views. For Does QIIME OTU Table gives idea about relative abundance?
Great Question 19 months ago, created a question with more than 5,000 views. For Core And Pan Genome Comparative Analysis
Student 2.3 years ago, asked a question with at least 3 up-votes. For Core And Pan Genome Comparative Analysis
Great Question 2.3 years ago, created a question with more than 5,000 views. For How To Decide Best Docking Conformation From Autodock Results?
Great Question 2.3 years ago, created a question with more than 5,000 views. For How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Does QIIME OTU Table gives idea about relative abundance?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Does QIIME OTU Table gives idea about relative abundance?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: How Can I Download Or Get A Pathway List From Kegg
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Does QIIME OTU Table gives idea about relative abundance?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Does QIIME OTU Table gives idea about relative abundance?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Does QIIME OTU Table gives idea about relative abundance?
Great Question 4.0 years ago, created a question with more than 5,000 views. For Software For Analysis Of Bacterial Genomics.
Student 4.0 years ago, asked a question with at least 3 up-votes. For Software For Analysis Of Bacterial Genomics.
Great Question 4.0 years ago, created a question with more than 5,000 views. For Phylogenetic Analysis By Maximum Likelihood (Paml) : Upon Phylip Input Yn00.Clt Program Not Running.
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Phylogenetic Analysis By Maximum Likelihood (Paml) : Upon Phylip Input Yn00.Clt Program Not Running.
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Sample ORTHOMCL run on my Fasta file.
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How To Derive Pan Proteome
Great Question 4.0 years ago, created a question with more than 5,000 views. For How To Decide Best Docking Conformation From Autodock Results?
Great Question 4.0 years ago, created a question with more than 5,000 views. For How To Decide Best Docking Conformation From Autodock Results?
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Popular Question 4.1 years ago, created a question with more than 1,000 views. For How Much Time Is Required For 1 Nanosecond Md Simulation.
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