I have analyzed gut flora of Helicoverpa and found B. pumilius, with some strain identification by 16S rDNA analysis.
I want to check these strains via nucleotide diversity by DNA sp software. I am looking reference sequences of 16S rDNA of those strains. Can you please suggest other than NCBI data base for getting reference sequences for diversity analysis of these strains?
BTW, Venkatachalam, EZ-taxon (ezbiocloud now) is a special database for valid species and common uncultured clones (the modern verison). LPSN - is a database of valid taxa, not sequences. Thus, both useful for understanding whether your microbe new or not.
You Can collect reference type strains from EZ Taxon-E database, Strain info, or LSPN .....by the way your from which dept in IARI??
NCBI nt databases. ARB-Silva. RDP. Greengenes (but they stopped updating since 2010 as I remember)
BTW, Venkatachalam, EZ-taxon (ezbiocloud now) is a special database for valid species and common uncultured clones (the modern verison). LPSN - is a database of valid taxa, not sequences. Thus, both useful for understanding whether your microbe new or not.
Be careful using 16S rRNA to check strains and species, frequently strictly related species has nearly identical 16S sequences. You can check greengenes database or RDP and verify if 16S sequences of the strains you are interested are available.
If you need more details you can check the paper we have recently published, there are some details on species belonging to the Lactobacillus genus having very similar 16S rRNA sequences.
http://link.springer.com/article/10.1007%2Fs00253-014-5795-3
Dear friends..thank you for information u provided especially with article..I'll go thorough on it ..get back to u shortly..many thanks Stefano.
Dear Kublanov,
What you told is very true, BTW, EZ taxon is having up to date validly published type strains, where you can rely on most compared to NCBI nt where you can find lot of junk sequences also. I belive you can retreive sequences from Eztaxon also.
As you told RDP and Greengenes is also best but it is not up to date...
- Badges
- Science topic
- Similar topics
- Biological Science
- Zoology
- Invertebrate Zoology
- Entomology