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Problems in DNA barcoding

Dear all, This group is intend to solve problems occurred while analyzing barcode sequences and using appropriate method of analysis.

Website: http://problemsindnabarcoding
Location: Pune, Maharashtra, India
Members: 85
Latest Activity: 12 minutes ago

Discussion Forum

Sequence error 3 Replies

I have doing my deposition of sequence in the NCBI, but when one of the sequence is deposited I have got a message stating that some or all of the sequences contain reading frame shifts…Continue

Started by sreejith kanholi. Last reply by sreejith kanholi on Sunday.

DNA Barcoding in bacteria 2 Replies

Hai to all, I need 100% details on DNA Barcoding of bacteria from soil samples by culture independent methods. I have a problem from the beginning of bacterial DNA extraction to Pyrosequencing. So,…Continue

Started by D. ESTHER LEBONAH. Last reply by D. ESTHER LEBONAH Nov 20, 2013.

MatK gene region in angiosperm 5 Replies

Dear all,I am currently working on DNA Barcoding of some plants (belonging to Angiosperm). Fistly ı did not use DMSO for MatK gene region. But sequence results are not good and then ı use the DMSO,…Continue

Started by Handan. Last reply by Paula May 29, 2012.

primer 5 Replies

Hello sir/madam,                     I am currently working on  DNA Barcoding of the odonata.Am in the initial stages of sample collection and only limited referece are available on this area of…Continue

Tags: gene, CO1, odonata, primer

Started by Dr.C.VADIVALAGAN. Last reply by Anoja Kurian Jan 6, 2012.

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Comment by Prasanna Kumar on December 7, 2011 at 11:53am

@ Hi Chelzie

I am please to know that u have made progress in bacterial barcoding. I like to see ur abstracts as i could not download it from the web. I missed the conference due to last minute emergency. Else we would heve met. Plz mail the your abstracts to marinemicrobiology@gmail.com. As rpoB's efficacy in delineating bacilli and other bacterial species has been well established, what are the difficulties you are facing? What sort of improvements should one be expecting? like to discuss further with u. Thanx for the reply.

Comment by Gaikwad Swapnil Sopan on December 7, 2011 at 1:11am

Hi Prasanna Kumar,

Story of bacteria is really different.....if you look at the intraspecies divergences. I do agree with  Chelzie Crenna Darusallam   rpoB is better marker. However, for bacteria MLST approach is followed i.e. multiple locus sequence typing and thus status of new species is confimed. And further this is approved by DNA DNA hybridisation.

I hope this will help you,

Keep posting,

Swapnil

Comment by Chelzie Crenna Darusallam on December 7, 2011 at 12:46am

Hi Prasanna Kumar,

I am working in marine bacteria and assessed DNA barcode (rpoB gene) to identify (you can found my abstract poster in the conference web -C7). The rpoB showed promising result however as the new marker it still need some improvement(s). The idea for DNA barcode for bacteria is find the core gene (as has been described in Rodoni's presentation in the conference)..I am very pleased to discussed further with you.

Comment by Prasanna Kumar on December 6, 2011 at 11:57pm

Hi hope all had blast in fourth conference. As dna barcoding technology have been expanded and it almost touched every aspects of tree of life, but one group that remained isolated is bacteria. Although the problems of barcoding bacteria is discussed @ http://www.ccdb.ca/pa/ge/research/domains-of-life/archea-and-bacteria, the article promises to define a barcode gene for this prokaryotic group in near future. I wish to know is there any such gene in practice? I am very much interested to define and produce DNA barcodes for bacteria, especially for marine bacteria. I hold 84species of freshly isolated marine bacteria from bay of bengal and its respective 16SrRNA sequences. Many species in same family shared 2% to 0.5% variation which overcame the species boundary of 3% variations. I kindly request all members in this group to help me define and target a particular gene for bacterial barcoding. I have rpoB gene in mind, and have either positive points nor negative points to support or oppose it. So please help me to sort out the problem? could this be solved?, is another question poping up now.

:-)

Thanks for the reply.

Comment by Gaikwad Swapnil Sopan on April 2, 2010 at 1:19am
Yes, I have checked the orientation, it is prefect. But I can't deny the fact of pseudogen. i hope to solve the same.
Thanks for the response. Hope to see more inputs from you.
Keep posting.
Comment by Julie Stahlhut on April 1, 2010 at 11:23am
Hi, Gaikwad! I've seen this too, and here are two suggestions:

First, if you're assembling forward and reverse sequences from tracefiles, make sure that your DNA analysis program has not reversed their directions. If it has, it's usually easy to find a "reverse" function to put the sequences in their proper orientations. This often solves the problem.

Another possibility is that you are amplifying pseudogenes (numts). This may be more difficult to solve; you might have to try amplifying and sequencing with different primers.

Which insect taxa are you trying to barcode?


-- Julie Stahlhut
 

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