Question: What Are The Length Of 16S And 18S Rdna Regions And How Useful Is 454 Covering Their Length
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gravatar for rebekahnewstead
6.1 years ago by
rebekahnewstead0 wrote:

Hi, can anyone help.

I am struggling to find how long sequences usually are for 16s cyano and 18s euk rDNA. I hope this deesn't seem a silly question. I would like to find out so I can evaluate the usefullness of 454. I hope someone may be able to help, thanks

metagenomics sequencing • 8.4k views
ADD COMMENTlink modified 6.1 years ago by vijay1.5k • written 6.1 years ago by rebekahnewstead0
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gravatar for Josh Herr
6.1 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

They are roughly 1500 bp average for 16S and about 1800 bp for 18S. These aren't standard, so you can get some that differ a little in length, even within a single taxon. I assume you're asking about metagenomic uses, so for 454 you can get a solid chunk of them in a study with two primers and get a good assessment of diversity with specialized databases. More studies have investigated the 16S for 9 hypervariable regions of resolution (for example, see: Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing), than the 18S, but you should get fair resolution for both using 454 or Illumina at current sequencing lengths.

ADD COMMENTlink written 6.1 years ago by Josh Herr5.6k
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gravatar for Bert Overduin
6.1 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

Please see: http://en.wikipedia.org/wiki/Ribosomal_RNA (paragraph "Prokaryotes vs. Eukaryotes").

ADD COMMENTlink written 6.1 years ago by Bert Overduin3.6k
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gravatar for vijay
6.1 years ago by
vijay1.5k
Chennai
vijay1.5k wrote:

I endorse what Josh has added... Though the lengths of 16s and 18s genes are around 1500 and 1800 respectively , getting them completely sequenced is tough considering the read lengths produced by various NGS platforms. However by targetting a very specific hypervariable region(say v3 or v6 in case of 16s) which are about ~180-220 bp in length, 454 or Illumina can definitely give a good throughput which can analysed various workflows that are available.

ADD COMMENTlink written 6.1 years ago by vijay1.5k
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