Biswajit Bose

15 Questions 22 Answers 0 Followers

Questions related from Biswajit Bose

How to concatenate different coding and non-coding regions to perform neighbor joining (NJ) analysis in MEGA?

I have six different coding and non-coding regions and I want to concatenate them for the NJ analysis in MEGA so that I can get a NJ tree and calculate theta, theta prime, coalescent depth and...

27 June 2017 5,659 1 View

What are "Unverified" sequence in Genebank? Can I take those unverified sequences from Genebank for my phylogenetic analysis?

I am working on molecular phylogeny in the order level. When I am extracting the sequences from NCBI Genebank, I found there are lot sequences marked as unverified. For concratenation of multiple...

25 May 2016 2,650 7 View

How do I perform ecological niche modelling of threatened medicinal plants?

I am working on some threatened medicinal plants of Himalaya. I have all the latitude and longitude coordinates throughout the distribution of my study plants. I want to work on ecological niche...

08 October 2015 1,093 12 View

How do I deal with reading frame-shift in a coding sequence during sequence submission in genebank?

While submitting a protein coding nucleotide sequence in genebank, some sequences are sent back to me saying that there are reading frameshift problem in that nucleotide sequence. How to detect...

17 July 2015 3,521 2 View

Can I differentiate between closely related plant species?

Kindly could anybody suggest any highly variable markers for discrimination for closely related plant species/lower taxonomic level identification. If DNA barcoding could able to go at that level?...

17 July 2015 2,291 14 View

How to deal with the problem in Internal transcribed spacer 2 amplification?

I am working on some plants from Valerianaceae family(angiosperms). I have already sequenced rbcl, matK and two inter-genic spacer regions. I want to amplify ITS1 and ITS 2 regions. Here,...

16 September 2014 5,008 7 View

Can you help me with the operation of Mr Bayes software and the procedure for Nexus file conversion?

I want to use Mr Bayes for Bayesian inference model choice across a wide range of phylogenetic and evolutionary models (MCMC analysis). Which software will be best to convert the alignment files...

21 July 2014 7,314 3 View

Can anybody tell me the range of soil moisture content, soil OC and N to demarcate the forest types with emphasis on alpine region?

I am working on some plant species from high altitude Himalayan region. I have done soil moisture content test, organic carbon, nitrogen test for those plants. I think there is a relation between...

27 May 2014 3,997 4 View

Which explant should I use as a starting material in a plant tissue culture experiment?

I saw many papers that started with seed germination to achieve the in vitro cultures and from the in vitro raised seedlings they took leaves, petioles and apical buds for further multiplication....

03 April 2014 1,638 12 View

Can someone advise in the field of phylogeography and sample size?

I am working on an alpine medicinal plant collected from all over its geographical distribution around the world. Now I want to do a phylogeographical study as I have samples (10-12/site). Can I...

15 February 2014 6,242 10 View

Is genetic stability maintained from seed derived plantlets in vitro or are there will be somaclonal variation among them?

I have done asymbiotic seed germination of an orchid sp and got protocoms from them and finally seedlings. I got protocorm like bodies (PLBs) from pseudobulb segments and internodal segments taken...

08 December 2013 4,282 1 View

How speciation occurs in course of Evolution?

If anyone wanted to trace speciation process over geologic time, are there any molecular techniques to do that? Exactly when and how those species get separated over time? If two species are more...

17 March 2013 664 9 View

Are there any labs working on plant total genome size estimation by flow cytometry?

I want to estimate plant total genome size by flow cytometry. Are there any reliable, simple protocols to estimate 2C content?

24 February 2013 5,950 3 View

Can any one suggest any protocols for plant 2C content estimation by flow cytometry from leaf segments?

I want to estimate the total genome size of my study plants. These plants are found in the high Himalayas. Are there any reliable, simple protocols for the estimation of total genome size of plant...

22 February 2013 1,542 2 View

Can anyone please explain what I have to do exactly to avoid primer dimer?

I am trying to amplify RbCl gene with forward primer (Tm 54) and Reverse primer (Tm 63). But, I am getting primer dimers with different concentations of MgCl2 (10,12.5,15 and 25 mM). With 15 mM I...

21 February 2013 2,587 54 View