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
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written
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Mcdenzlix •
2 answers
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 ?
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written
by
Pierre Lindenbaum
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...)
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You got some nice answer for your previous question. Can you please validate one ?
what do you mean by 'rna genes'?