User: Nari

gravatar for Nari
Nari840
Reputation:
840
Status:
Trusted
Location:
United States
Twitter:
BloodTypo
Last seen:
2 months ago
Joined:
5 years, 7 months ago
Email:
n**********@gmail.com

PhD Student interested in Human Microbiome, NGS.

Posts by Nari

<prev • 177 results • page 1 of 18 • next >
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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 4 months ago by Nari840
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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 4 months ago by Nari840
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Comment: C: comparison between two orthologs
... mention which tool you used for ortholog prediction ...
written 4 months ago by Nari840
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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 5 months ago by Nari840
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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 5 months ago by Nari840
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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 5 months ago by Nari840
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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 5 months ago by Nari840 • updated 5 months ago by Michael Dondrup44k
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Comment: C: Automatically Getting The Ncbi Taxonomy Id From The Genbank Identifier
... This may work only if the url goes **https** not http, as ncbi has turned https only in 2017. ...
written 6 months ago by Nari840
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Answer: A: how to use pan-genome in python?
... Go to https://omictools.com/pangenomics-category . There are plenty of them, search for python in description for each tool. It also includes my own tool **BPGA** (*second in the list*), but it's perl based. ...
written 16 months ago by Nari840
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Comment: C: Comparative Bacterial genome alignments
... Yeah try **subset analysis** and create groups according to environment. Refer to [detailed documentation of BPGA.][1] Also refer to [BPGA Userguide][2] for subset/grouping analysis. [1]: https://sourceforge.net/p/bpgatool/wiki/Home/ [2]: https://sourceforge.net/projects/bpgatool/files/BPGA%20 ...
written 17 months ago by Nari840

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