Question: How Do You Find The Available Number Of Insect And Metazoan Genomes?
0
gravatar for biostar
6.3 years ago by
biostar150
biostar150 wrote:

Sorry if you find this question silly enough to be annoying. I have been looking for a reliable source(of course NCBI) to find the total number of published genomes of insecta and metazoans. I tried NCBI and found 731 genomes of insects indicated (not so clearly mentioned) there. I need the number of genomes for both metazoans and insecta that have their proteins annotated. Could any of you please suggest me the source/link or let me know the total number of published insect and metazoans genomes? Thank you for your help!

genome protein • 1.7k views
ADD COMMENTlink modified 6.3 years ago by Pierre Lindenbaum129k • written 6.3 years ago by biostar150
3
gravatar for Pablacious
6.3 years ago by
Pablacious620
Cambridge, UK
Pablacious620 wrote:

I would use the NCBI Taxonomy, where you can select a particular taxonomic domain and then switch on the counts of available genomes, publications, etc.

Go to http://www.ncbi.nlm.nih.gov/taxonomy/?term=insects

click on Hexapoda and then on the grey rectangle full of check boxes choose what you want (like genomes), and then click on the Display button. You should see the number of genomes per level of taxonomy. I agree though with Biojl that it might not be updated.

You could also take a look at the genomes available page at the EBI:

https://www.ebi.ac.uk/genomes/

ADD COMMENTlink written 6.3 years ago by Pablacious620
2
gravatar for Biojl
6.3 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

I think that due to the high speed of sequencing there is no updated source. You can find some in Ensembl (Ensembl, Ensembl genomes, etc) or NCBI but not all of them are there. Some of them are uploaded but lack a publication, like the polar bear, hidden here http://gigadb.org/. There was a nice database but is not updated at all: http://genomesonline.org/cgi-bin/GOLD/index.cgi

ADD COMMENTlink written 6.3 years ago by Biojl1.7k
1
gravatar for Pierre Lindenbaum
6.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

go to NCBI BioProject https://www.ncbi.nlm.nih.gov/bioproject/limits

check Organism Groups > Insects

export the result as XML and grep the uniq Taxon-Id

ADD COMMENTlink written 6.3 years ago by Pierre Lindenbaum129k

Thank you so much!

ADD REPLYlink written 6.3 years ago by biostar150
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