User: Penny Liu

gravatar for Penny Liu
Penny Liu30
Reputation:
30
Status:
New User
Location:
Taiwan
Website:
https://www.behance.ne...
Last seen:
4 hours ago
Joined:
2 years, 6 months ago
Email:
e**********@gmail.com

Posts by Penny Liu

<prev • 23 results • page 2 of 3 • next >
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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 2.2 years ago by Penny 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 2.2 years ago by Penny 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 2.2 years ago by Penny Liu30 • updated 21 months 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 2.2 years ago by Penny Liu30 • updated 2.2 years 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 2.3 years ago by Penny Liu30
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Comment: C: Choosing specific candidate genes for phylogenetic tree construction
... The reason is multiple sequence alignment (MSA) program - ClustalW is extremely limited when in regards to multiple whole genome sequencing. ...
written 2.3 years ago by Penny Liu30
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Comment: C: Choosing specific candidate genes for phylogenetic tree construction
... I'm a little confused by your last comment. What is the main purpose of finding plasmids or other mobile elements? Thanks again! ...
written 2.3 years ago by Penny Liu30
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Comment: C: Choosing specific candidate genes for phylogenetic tree construction
... Thank you so much for providing me with useful comments. Choosing the nine virulence genes, or even more virulence factors (VFs) are belong to feature selection or clustering problems. Moreover, the currently selected of nine virulence genes may have degree of discrimination but I think it's not pe ...
written 2.3 years ago by Penny Liu30
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Comment: C: Choosing specific candidate genes for phylogenetic tree construction
... You are right! This study we want to analyze virulence and resistance from *Serratia marcescens*. ([cite][1]) However, in this post we aim to reconstruct the phylogenetic history of the *Serratia marcescens*. Any comments and suggestions would be appreciated :) [1]: http://tggs.stat.sinica.edu. ...
written 2.3 years ago by Penny Liu30
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Choosing specific candidate genes for phylogenetic tree construction
... I want to compare our strains [VGH107][1] with other *S. marcescen* strains phylogenetic relationship. This selection contained both nonpathogenic (environmental, agricultural, and industrial) as well as pathogenic strains of various pathotypes. From my understanding, 16S sequences are not suitable ...
phylogenetic mvlst virulence factors sequencing written 2.3 years ago by Penny Liu30 • updated 2.3 years ago by kloetzl1.0k

Latest awards to Penny Liu

Popular Question 6 months ago, created a question with more than 1,000 views. For Search COGs from the EggNOG collection
Popular Question 7 months ago, created a question with more than 1,000 views. For Extract all bacteria sequences from the nr database
Autobiographer 16 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 19 months ago, created a question with more than 1,000 views. For Extract all bacteria sequences from the nr database

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