User: Nari
Nari • 880
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- 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
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... 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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... 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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... 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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... 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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... 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/ ...
written 3.1 years ago by
Nari • 880
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... 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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... 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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... 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 ...
written 3.1 years ago by
Nari • 880
• updated
3.1 years ago by
Michael Dondrup ♦ 48k
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