Why do we need to remove/delete the 3rd codon positions in the Protein Coding genes?

More Muzafar Riyaz's questions See All

How to do rat bone Immunofluorescence, Please suggest?

Hello, I have been trying to do a rat bone Immunofluorescence histology study. But not able to find a successful protocol till now, Any suggestions? Rat bone: Decalcifies Embedding: Cryo

26 January 2021 4,165 3 View

How pH will effect the overpotential for a reaction like OER,ORR etc?

From a theoretical perspective, when we study the electrocatalytic efficiency of a modeled catalyst, we calculate its overpotential. Here the contribution of pH to energy change for each reaction...

08 December 2020 8,726 3 View

Can matter and antimatter be present in equal amounts on large scale structure of the universe?

If we believe in baryon number conservation as a universal law. The matter and antimatter must have created in equal amounts during the first few microseconds of big-bang. Therefore the antimatter...

16 June 2016 8,377 9 View

Is anybody using a manual method for DNA isolation from plasma?

I want to isolate manually (without kit) cell free fetal DNA (cffDNA) from maternal plasma at mean gestational age of 19 weeks. Kindly suggest the protocol.

09 April 2014 2,516 1 View

Does anyone have a recommendation for yeast reporter gene plasmid/protocol?

Hi, could anyone recommend a plasmid and/or protocol for reporter gene assay in S. cerevisiae? I want to assess the effect of growth conditions on a transcription factor, so I want to clone it`s...

01 March 2021 210 1 View

Where to find data on trees in tropical agroforestry?

Hi, I'm looking for data (mainly related to management: growth rate, canopy size, soil and climate preferences, etc.) about tropical trees used in tropical agroforestry. Have you ever heard about...

28 February 2021 7,356 8 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

Does the phylogenetic tree making tool IQTREE use evolutionary placement algorithm?

For my master thesis I am conducting a phylogenetic research and for this I'm using tools like MEGA, IQTREE, FigTree, etc to make a phylogenetic tree. I wanted to know if IQTREE integrates the...

14 February 2021 1,541 2 View

Should GFP sequence be cut together with the IRES sequence?

Hello. I have a viral plasmid which contains a bicistronic region: CMVprmtr-GFP-IRES-PuroR. I would like to cut out the GFP sequence to get rid of the green fluorescence. In this case, would it be...

02 February 2021 1,644 7 View

How to do DNA normalization based on qPCR values?

Hi Everyone: I have a question regarding to qPCR. I am trying to do RT-PCR, and I want to have equal amount of input DNA for my RT-PCR, so I normalize my DNA input based on qPCR values of a...

31 January 2021 6,977 4 View

Is there an alternative to PGLS that considers phylogenetic signal when calculating the estimated value?

I have been working on a study trying to estimate body mass in mammals using a skeletal proxy in R. My dataset has high phylogenetic signal (Pagel's Lambda = 0.9) and I am interested in removing...

26 January 2021 6,997 3 View

Can someone help me identify the bands?

The samples are replicates (4) of total RNA from HEK-293 T cells. The ladder is a 1kBp ladder on a 1% native agarose gel buffered with 1x TAE. From my searches, there should be two sharp bands at...

15 January 2021 4,712 4 View

Should I add a promoter upstream of my CRISPR-inserted gene?

Hello, I want to insert a gene into my cells using sgRNA, Cas9, and an HDR template. The gene that I will insert into has its own promoter. Because I will cut the gene downstream of its start...

14 January 2021 1,170 2 View

Tayná da Silva Fiúza

The 3rd position of a codon, also called the wobble position can vary quite a lot. A nucleotide in this position can have many types of non Watson-Crick base pairing. In phylogenetics the removal or coding of this position is employed to reduce compositional heterogeneity, as it can drasticallly change the trees obtained.

Read about it over here:

Yang H, Li T, Dang K, Bu W. Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera). BMC Genomics. 2018;19(1):264. Published 2018 Apr 18. doi:10.1186/s12864-018-4650-9

Breinholt JW, Kawahara AY. Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data. Genome Biol Evol. 2013;5(11):2082-92. doi: 10.1093/gbe/evt157. PMID: 24148944; PMCID: PMC3845638.