Actually, I want to find the the16S rRNA for "Anoxybacillus flavithermus strain TNO-09.006". Its whole genome sequence is present in the database but i want 16S rRNA sequence to do phylogeny along with other similar strains e.g. Anoxybacillus flavithermus NBRC 109594, Anoxybacillus flavithermus subsp. yunnanensis str. E13 etc. This is is what I am unableto do. Therefore, i would appreciate if you please help me in this matter.
Thank you
http://www.ncbi.nlm.nih.gov/genome/genomes/1710
You could use the Silva database http://www.arb-silva.de/search/, this will give you a link to download your file as fasta.
You can follow links from taxonomy browser to genbank sequence, customize view to show features, search for 16S rRNA and get to this:
http://www.ncbi.nlm.nih.gov/nuccore/440214640?from=9904&to=11463&sat=4&sat_key=131901788
That is bases 9,904 to 11,463 jn the complete genome entry, which is the 16S rRNA gene sequence.
- At first, you can follow the link suggested by Brian Thomas Foley:
http://www.ncbi.nlm.nih.gov/nuccore/440214640?from=9904&to=11463&sat=4&sat_key=131901788
- Click the "Run BLAST" link on the right hand-side pane
- In the BLAST result, choose sequences you want to collect and download them in FASTA format.
If you follow Quan Thai Ke's excellent advice, you may also find it useful to rename the sequences in the FASTA file. Saving the BLAST hits in FASTA format, they will have long names with characters such as ":" in the names which are not allowed in phylogenetics programs.
There is a nice tool for renaming sequences in FASTA files:
http://veb.lumc.nl/SNAD/
SNAD, Sequence Name Annotation-based Designer
To convert names like this:
>gi|630256956|gb|KJ722463.1|:1-1537 Anoxybacillus flavithermus strain 51THE31 16S ribosomal RNA gene, partial sequence
to this:
>Anoxybacillus_flavithermus_KJ722463
I have attached the renamed alignment, and a tree built from it.
Hello Brian and Quan!
Thank you for your help and attention. Your answers are really helpful. However, I want to ask from Dr. Brian, that how did you find the sequence range from 9,904 to 11,463 bp. Furthermore, from where I can find the links on taxonomy browser to genbank sequence as you mentioned in your comment.
And Quan! Can you please tell me the procedure to download the sequence from BLAST results in detail?
Thank you once again to both of you.
Arslan
To find the 16S rRNA gene in the genome, I just went to the GenBank entry for the genome you listed:
http://www.ncbi.nlm.nih.gov/nuccore/440214640
Then in the upper right, under "customize view" I asked to see genes and rRNA features and the sequence, then searched for 16S ribosomal, then selected the first one I found. In this genome there are several copies of the 16S rRNA gene, as there are in most bacteria. But in my experience a single bacterial genome usually contains identical copies of the 16S rRNA gene. Another one in this genome is at bases 178,077 - 179,636:
rRNA 178077..179636
/locus_tag="AF6_RS01100"
/old_locus_tag="AF6_rRNA14"
/product="16S ribosomal RNA"
The rRNA is a "hot link" to see just those bases. And then when you are viewing just those bases, you can click the BLAST button, to find other highly similar sequences. Select all, or a sample of them, and then download the FASTA alignment. Rename the sequences using SNAD and then view the alignment to make sure it looks good before building the tree.
Most phylogenetics packages such as MEGA and DAMBE include a multiple sequence alignment viewer built in. But stand alone multiple sequence alignment editors such as ALIVIEW for Mac or BioEdit for Windows, are essential if you do much sequence work. In addition to making it easy to edit alignments if the BLAST result, or MUSCLE or MAFFT results need a little touch-up, the editors also provide features for many other tasks such as format conversion (export alignment in FASTA, PHYLIP, NEXUS and other formats), translate DNA to protein, sort sequences by similarity, and many other things.
http://www.ormbunkar.se/aliview/
http://www.mbio.ncsu.edu/bioedit/bioedit.html
http://www.megasoftware.net/
http://dambe.bio.uottawa.ca/dambe.asp
http://www.kuleuven.be/aidslab/phylogenybook/home.html
Dear Dr. Brian!
I really appreciate this help of you. Finally I am done with my assignment.
Best,
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