User: Yi-Ting Liu

gravatar for Yi-Ting Liu
Yi-Ting Liu30
Reputation:
30
Status:
New User
Location:
Taiwan
Last seen:
1 week, 2 days ago
Joined:
1 year ago
Email:
e**********@gmail.com

Posts by Yi-Ting Liu

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Species identification via gilist
... My extract method same as you. This process can take several hours to complete. I added multiple keywords ([term=whole+genome+bacteria][1]) to narrow down the search scope. [1]: https://www.ncbi.nlm.nih.gov/protein/?term=bacteria%20complete%20genome ...
written 6 weeks ago by Yi-Ting Liu30
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Comment: C: Species identification via gilist
... You're right. The word `gi` is redundancy. I removed the redundant data from text file, then the problem is solved. :) ...
written 7 months ago by Yi-Ting Liu30
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Species identification via gilist
... I want to narrow down the blastn search against `nt database` using `gilist`. I already got all taxids of bacteria (`taxid 2`) and extacted GIs with `csvtk` ([Please refer to this][1]). The next step was to proceed bacterial species identification. When I run blastn -query query.fasta -db /p ...
taxid blast gilist written 7 months ago by Yi-Ting Liu30
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Comment: C: Extract all bacteria sequences from the nr database
... [TaxonKit][1] worked out perfectly. However, there's something strange here. I already got all taxids of bacteria (taxid 2) and extacted accessions also GIs with csvtk ([Please refer to this][2]). Subsequently, I [extracting nr sequences][3] as the next step `$ blastdbcmd -db nr -entry all -outfmt ...
written 7 months ago by Yi-Ting Liu30
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Comment: C: Extract all bacteria sequences from the nr database
... The page displaying title is extract all protein sequences from the NCBI nr database. How to get DNA sequences rather than protein sequences? ...
written 8 months ago by Yi-Ting Liu30
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Comment: C: Extract all bacteria sequences from the nr database
... Hi, I got same error even use the `($2 == 9606)`. ./blastdbcmd -db nr -entry all -outfmt "%g %T" | awk ' { if ($2 == 9606) { print $1 } } ' | ./blastdbcmd -db nr -entry_batch - -out human_sequences.txt ...
written 8 months ago by Yi-Ting Liu30
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Comment: C: Extract all bacteria sequences from the nr database
... > BLAST Database error: No alias or index file found for nucleotide > database [nr] in search path Can you explain what vital steps I missed out? Thank you again. Getting all taxids of bacteria ([taxid 2][1]) ./blastdbcmd -db nr -entry all -outfmt "%g %T" | awk ' { if ($2 == 2) { print ...
written 8 months ago by Yi-Ting Liu30
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Extract all bacteria sequences from the nr database
... Is there a quick way to extract all bacteria sequences from NCBI non-redundant (NR) database using `blastdbcmd`? This command applies only to [extract all human sequences from the nr database][1]. How about in microbial sequences case? $ blastdbcmd -db nr -entry all -outfmt "%g %T" | \ ...
ncbi nr database bacteria written 8 months ago by Yi-Ting Liu30 • updated 12 weeks ago by jgl40
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Search COGs from the EggNOG collection
... I want to classified predicted genes using the COGs (Clusters of Orthologous Groups of proteins) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. The function annotation of COGs like the [publication][1] posted below. ![enter image description here][2] For performance reasons, the onl ...
eggnog alignment function annotation written 9 months ago by Yi-Ting Liu30 • updated 9 months ago by Lars Juhl Jensen11k
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Comment: C: Choosing specific candidate genes for phylogenetic tree construction
... non-pathogenic and pathogenic strains are contained all 9 virulence genes. ...
written 9 months ago by Yi-Ting Liu30

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Extract all bacteria sequences from the nr database

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