The Rna Genes Download

Question

[Mcdenzlix]

Given the species below whose genomes are fully sequenced and annotated in NCBI. I only need to obtain all the rna genes for further processing. someone out there with a script that can do the task perfectly. my last quiz went poorly because i never gave examples. well here are more than examples. Alternatively i may use 16S rna for the start. share that script someone...urgent help needed

Alicyclobacillus  acidocaldarius DSM 446
Anoxybacillus  flavithermus WK1
Bacillus  amyloliquefaciens  FZB42
Bacillus  amyloliquefaciens  DSM7
Bacillus  anthracis CDC 684
Bacillus  anthracis  STERNE
Bacillus  anthracis Ames 
Bacillus  anthracis CI
Bacillus  anthracis str. A0248
Bacillus  anthracis Ames ancestor
Bacillus  atrophaeus 1942
Bacillus  cereus 03BB102
Bacillus  cereus AH187
Bacillus  cereus AH820
Bacillus  cereus  ATCC 14579
Bacillus  cereus  ATCC 10987
Bacillus  cereus  ATCC 9818 
Bacillus  cereus B4264
Bacillus  cereus E33L
Bacillus  cereus G9842
Bacillus  cereus Q1
Bacillus  clausii KSM-K16
Bacillus  cytotoxicus NVH 391-98
Bacillus  coagulans  36D1 
Bacillus  halodurans  C 125
Bacillus  licheniformis ATCC 14580
Bacillus  megaterium  QM B1551
Bacillus  megaterium  DSM319
Bacillus  mycoides  
Bacillus  pseudofirmus  OF4
Bacillus  pumilus SAFR-032
Bacillus  selenitireducens MLS10
Bacillus  subtilis  168
Bacillus  subtilis  ATCC 6633
Bacillus  subtilis subsp. spizizenii str. W23
Bacillus  thuringiensis  BMB171
Bacillus  thuringiensis str. Al Hakam
Bacillus  thuringiensis serovar konkukian str. 97-27
Bacillus  tusciae DSM 2912
Bacillus  weihenstephanensis KBAB4 
Brevibacillus  brevis NBRC 100599

[Pierre Lindenbaum]

You got some nice answer for your previous question. Can you please validate one ?

[Giovanni M Dall'Olio]

what do you mean by 'rna genes'?

Answer 1

[Pierre Lindenbaum]

Use the NCBI utilities: ESearch and EFetch (many examples here, on biostar) with the following sample query:

"Bacillus  subtilis  168"[ORGN] biomol_mRNA[PROP]

unfortunately, many organisms are poorly annotated and you won't easily find the mRNA sequences. May be you could just filter the sequences using a size criteria with the [SLEN] operator ?

Answer 2

[Mary]

I can't give you a script, but I can offer the IMG resource as a way to quickly get RNA sequences. If you go to an organism detail page they offer a link that looks like this to get the RNA sequences.

Here's an example of one of the B. cereus strains: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=643692007

In the "Genes Total Number" section of the table there is a link to various breakdowns of the RNA sequences. You can click the hyperlinked number to get the list, and then do various operations on the results sets.

Keep in mind that is just one of the many strains that are listed there. I did a "find genomes" search for cereus, and sorted by "finished" to explore them.

Alternatively you could select the species and set that at IMG as your query subset, then do a gene search for the specific ones you want, export those all at once.

(Sorry to be late to this, I was away for Thanksgiving...)