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i wanna find a reference genome

i wanna find a pseudomonas aeruginosa reference genome fasta file and annotation file, but i search "pseudomonas aeruginosa" in ncbi, they are so many result.

genome
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written by Kidult • Kidult

http://www.ncbi.nlm.nih.gov/genome/187

Representative: Reference genome: Pseudomonas aeuroginosa PAO1 NC_002516.2

Searching for NCBI genomes yields the representative genome on the species page.

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written by Jenez Jenez

OK...Thank you!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

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written by Kidult • Kidult

Why oh why do people not read the instructions before they post an answer?

Please move this to a comment on 5heikki's answer. Click on the "Add Comment" gray button you see in that post, copy and paste the text from your answer above to that text box and then click the green "Add Comment" button.

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written by Ram Ram

I really really really really wanna zig-ah-zig-ah, but given that this is a scientific forum and not a pop song, I want to see adult language, with capital letters and full words.

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written by Emily Emily

First time I've seen anyone push you over the edge. Welcome to the club :)

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written by Ram Ram

@ Ram Sorry... I have readed the instructions befor i posted the "OK" answer, but they are nothing change in my screen, when I click the add comment botton or the ADD REPLY botton. I try it again, now. It's still nothing change in my screen (nothing green botton or text appear), but I realreally click the Botton. And I want to know how can I del my "OK" answer ? Any newer tutorial ? Sorry again.

@ Emily_Ensembl Sorry... Next time I'll watch out for that sort of thing, I'll pay attention to this... Thanks for your comment.

@ John Excuse my ridiculous Question. Thanks for your comment.

@ Jenez Thanks for your answer. Thank you !

@ venu The Pseudomonas Genome DB is so cool. Thanks thanks !!!!

@ 5heikki Your answer is so cool !!!!! Thanks for your answer ~~~

Maybe I submit the bad "Answer" again, I just want to thank you all. And I do sincerely apologize to you again, and thank you again.

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written by Kidult • Kidult

How to add comment: Apply this procedure to the relevant answer on this post.

How to add reply: Apply this procedure to relevant comments on this post.

Once you are done, a moderator will delete your old responses. You can do it yourself by using the moderate button (on the relevant post/comment), then selecting Delete post and clicking Submit, but we don't have a definitive tutorial/guide for it yet.

• 1 views • link
written by Ram Ram

1 answer 

#!/bin/bash
echo "Downloading refseq assembly summary"
(curl -# ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt > ./assembly_summary_refseq.txt)
if [ $? -eq 0 ]; then 
    grep -w "Pseudomonas aeruginosa" assembly_summary_refseq.txt | \
    awk -F '\t' '{if($11=="latest" && $12=="Complete Genome") print $0}' > \
    latest_Complete_Genome_Pseudomonas_aeruginosa_refseq_assemblies.txt
    COUNT=$(grep -c . latest_Complete_Genome_Pseudomonas_aeruginosa_refseq_assemblies.txt)
    echo "Found $COUNT complete genome level assemblies:"
    awk -F '\t' '{print $8","$9"\t"$20}' latest_Complete_Genome_Pseudomonas_aeruginosa_refseq_assemblies.txt
    exit 0
else 
    echo "There was a problem in data retrieval"
    exit 1
fi
  1. save as getPseudoInfo
  2. chmod +x getPseudoInfo
  3. ./getPseudoInfo

Output is info about 53 complete genome level P. aeruginosa assemblies: "Species, strain, ftp url where desired files reside"

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updated by Ram Ram • written by 5heikki 5heikki

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