Anyone knows the meaning of OTU value on phylogenetic tree?

More Yen Teng Tai's questions See All

Transcriptional or post-translational regulation?

I have came across a paper where they observed a delay timing of a drug inhibitory effect and insulin stimulatory effect respectively on purine synthesis, and thus, they suspected that the...

09 October 2018 10,065 0 View

How to process RNA-seq results?

I have obtained the RNA-seq results, which is in an excel file with all the fpkm values. May I know how do I check the gene expression profiles? Is there any software for this or I gotta manually...

04 May 2018 3,497 9 View

How to determine a protein is working downstream of another protein?

If overexpression of protein A can rescue the growth defect caused by mutation in protein B, can I consider protein A is working downstream of protein B? If yes, why is it so?

04 May 2017 7,659 24 View

Can anyone suggest method to extract membrane proteins?

Currently I am having problems in extracting membrane proteins (ammonium transporters), can anyone help? I used LDS in extraction and I did not heat the samples. Proteins in lane 1-4 seem like...

03 April 2017 916 20 View

Best temperature to dry DNA samples after ethanol precipitation?

I am preparing samples for BigDye sequencing. After PCR, I did ethanol precipitation to clean up the samples. In order to dry up the samples (after removing 70% ethanol), is it okay for me to dry...

09 October 2016 6,278 8 View

Overexpression of a gene is toxic to the cell? Why is it so?

Currently I am working on a new protein in fission yeast. Based on the predicted function, it is involved in transcription. We found that when this gene is overexpressed, the cell growth is...

06 July 2016 8,871 1 View

If one of the proteins in S.pombe was tagged with FLAG, is this pombe still considered as wild type?

One of the proteins in S.pombe that I am working on is tagged with FLAG, so can I still call this strain as wild type as it contains a fragment of foreign DNA? If no, what is the right term for it?

05 June 2016 8,239 3 View

Can I re-digest my digested PCR product?

I have digested my PCR product with NEB Not1 and Nde1 for 1hr. I have cut the band and purified the product. However I afraid the digestion is incomplete, can I re-digest them again? Is there any...

04 May 2016 2,801 17 View

Anyone has protocol for TaKaRa PrimeSTAR mutagenesis basal kit in English?

Hi there. Anyone has protocol for TaKaRa PrimeSTAR mutagenesis basal kit in English? I have tried to search online but I can only get a Japanese version.

02 March 2016 5,017 6 View

What are the characteristics of a broad host range plasmid?

May I know what are the characteristics of a BHR plasmid? Is this kind of plasmid occurs naturally or we can try to engineer a narrow host range plasmid to become one?

01 February 2016 7,302 0 View

How to learn more about SPSS and its Application?

I would like to learn more about SPSS and Its application especially in regards to data analysis. Please suggest me how I can learn more about it. Thank you so much.

11 August 2024 9,101 4 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

Text-Communication from the M1 Hand Area using BCI—and then there is Elon Musk?

Willett, Shenoy et al. (2021) have developed a brain computer interface (BCI) that used neural signal collected from the hand area of the motor cortex (area M1) of a paralyzed patient. The...

10 August 2024 7,180 0 View

Has anyone applied Python in the field of textile engineering for data analysis, automation, or smart textiles?

I'm currently exploring the application of Python in textile engineering, specifically in areas like data analysis, process automation, and the development of smart textiles. I'm interested in...

10 August 2024 7,429 2 View

Which Scopus Journal provides the most affordable fees?

"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....

10 August 2024 8,621 1 View

Seeking Advice on Viability and Execution of Undergraduate Thesis Topic?

Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...

10 August 2024 8,992 0 View

How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?

09 August 2024 7,718 0 View

Who will be moral responsible for the death of thousands of people in the event of an earthquake?

Who will bear moral responsibility for the deaths of thousands of people in the event of an earthquake? Weeks and months remain before the onset of strong earthquakes that bring death to...

08 August 2024 6,134 12 View

How are iso-frequency contours plotted?

Let's say we have a standard, regular hexagonal honeycomb with a 3-arm primitive unit cell (something like the figure attached; the figure is only representative and not drawn to scale). The...

07 August 2024 1,937 1 View

Mohammad Imran Shah

A phylogenetic tree is composed of branches (edges) and nodes. Branches connect nodes; a node is the point at which two (or more) branches diverge. Branches and nodes can be internal or external (terminal). An internal node corresponds to the hypothetical last common ancestor (LCA) of everything arising from it. Terminal nodes

correspond to the sequences from which the tree was derived (also referred to as operational taxonomic units or ‘OTUs’).

https://www.google.co.in/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=0CCUQFjAC&url=http%3A%2F%2Fbama.ua.edu%2F~molsyst%2Fpage2%2Fassets%2FBaldauf2003.pdf&ei=9KZcVL-GGNCCuwTtiYCgCQ&usg=AFQjCNFXvb9n74KuM1mwrLZQ3SqeZF6W9A&sig2=QaRwrOehM0eFn0XCXxWwng

Karel Sedlar

Are the source data from metagenomic study? 16S rRNA sequencing? This kind of visualization is awful and useless. I guess that numbers represents number of sequences assigned to node or leaf. E.g. Bacteria 421 means that there are 421 bacterial sequences that cannot be assigned on lower taxonony (we are able to say it's Bacteria, not able to say it's Firmicutes or Proteobacteria). Axoneus 16 means that we are able to identify 16 sequences of this genus.

AbdelRahman Zueter

Mohammad Shah........thanks for the article

Yen Teng Tai

Thanks to everyone who provides the information. I asked the company but still, they didn't give me any reply.

Oh ya...By the way, this is from metagenomic sample, the sequencing is only targeting on 16srRNA.

If the value is zero, what is this means?

Zero also agrees with my interpretation. That's why leaves cannot be 0. If a genus is metioned, it has to contain at least one sequence. Internal nodes can be with zero. For example Parachlamidiaceae are with zero, because all of them was assigned on the genus level, no ambiguous sequence on this level was found.

Okay, now I understand. Thank you very much for the information.

Sundaresan Natesan

Terminal node also referred to as Operational Taxonomic Unit (OTU).

Refer: http://www2.ib.unicamp.br/profs/sfreis/SistematicaMolecular/Aula08MetodosMatrizesDistancias/Leituras/ThePhylogeneticHandbookMatrizesDistancias.pdf