I want to construct a phylogenetic tree based on my protein of interest (that is huge). Recommendations for softwares that can handle long seqs?

More Shubha Suresh's questions See All

Gerber file extraction in CST?

I have a feed alone as one of the layer. When i try to extract that, I get the folloing error. Kindly help me , how to resolve the issue and extract the gerber file

29 February 2024 3,772 2 View

Why do we see two zeta potential peaks even when the size distribution is monodispersed?

The emulsion of my sample has 0.08 polydispersity with an average size of 130 nm and only one peak (100 % intensity) both in DLS and MADLS. Nevertheless, I see two zeta potential populations....

20 February 2024 2,636 4 View

Can Bavistin be incorporated into microalgae media?

can Bavistin be incorporated into microalgae media against fusarium?

20 February 2024 3,488 0 View

How to retrive the green pigment in bleached microalgae in chu 10 plate containing antimycotic solution?

under the addition of antifungal, the microalgae did not have significant green pigment in the petriplate and cells looked bleached in petriplate. on microscopic analysis few cells were found to...

20 February 2024 6,788 0 View

Does the total mass contain both matter and antimatter masses?

If the total mass is interdependent, then does the total mass contain both matter and antimatter masses like this: Mass = Matter × Antimatter. E.g. (hypothetical), The Proton's mass ==...

17 January 2024 9,945 3 View

What is an appropriate Panel data estimation method if t=20 and i=20?

In panel data estimation if t=20 and i=20, do we necessarily need to test for stationarity, co-integration and causality. What is best method to estimate the model with this data set, if one is...

30 November 2023 6,086 0 View

Can I have a case on a social entrepreneur based in Mumbai authored by my co-author and I reviewed on ResearchGate?with my co-author?

I pioneered the courses on Start Your Business and Grow Your Business in India as Chairperson, Center for Entrepreneurship, SPJIMR, Mumbai. My colleague at SPJIMR , Dr. Nirja Mattoo set up the...

30 October 2023 5,805 2 View

What are the methods for analyzing trihalomethanes in water other than gas chromatography and liquid chromatography?

for monitoring disinfection byproducts in drinking water

12 October 2023 8,613 3 View

What are some common methods for quantifying the concentration of silver on a membrane surface before leaching test?

We can use EDX to measure the silver concentration before and after leaching test to know amount of silver leached. However, the concentration of leached silver from membrane is measured using...

09 September 2023 8,339 1 View

What are the recent studies in earthern structures and construction?

Suitability of Soil Sustainable alternative to Stabilizer and soil Pre and post construction issues and difficulties Durability of recent earthen construction

04 September 2023 9,749 0 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

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

Does crude extraction using NaOH and Tris work well with Fungi?

I'm trying to find a DNA extraction method for fungi that does not require equipment and heating. Is there anyone who can suggest an alternative option? Thank you

08 August 2024 4,733 2 View

Why after performing site directed mutagenesis ,I don't see any colony after transformation?

I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...

05 August 2024 9,059 3 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

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05 August 2024 6,787 4 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,079 0 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

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30 July 2024 6,420 1 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 View

Could you try using PeptiCloud and see if it's a useful tool for biology research?

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28 July 2024 4,762 2 View

Should the amount of DNA input used for ChIP-seq library preparation be matched between the control and experimental groups?

Hi all. As a beginner in ChIP-seq experiments, I hope you understand that the following questions might be somewhat basic. I am planning to perform ChIP-seq or MeDIP-seq analysis to investigate...

28 July 2024 6,938 1 View

Peter Ulz

You could try Clustal-Omega: http://www.ebi.ac.uk/Tools/msa/clustalo/ . They specify a limit of 4000 sequences but I do not see a limit on sequence length

Arun Kumar Jaiswal

you can also try MEGA- Molecular evolutionary genetics analysis tool

Pankaj Kumar Singh

You can try MAFFT server or its standalone version. I

http://mafft.cbrc.jp/alignment/software/

Shubha Suresh

Thank you all for the suggestions. MEGA worked well.