Alignment multiple genes

More Tomi Kasayev's questions See All

Found that there was a multiple band when amplifiying targeted gene ?

i few days ago amplified specific gene using PCR with specific primers, but there was a multiple band in electrophoregram i found. out of 10 sample amplified, there was multiple band and there was...

18 February 2021 5,404 5 View

How do i remove dimer primer when amplifiying DNA because i see on the electrogram of DNA ?

when i saw my DNA target on the electrogram there was a dimer primer below on DNA target. how do i remove it ? what should i do ? thanks

03 February 2021 5,509 3 View

Heating graphite powder and chrystal salt (rose salt)?

Hi! I'm planning of mixing graphite powder (for artists) with powdery glass and melting that fine mixture in sealed kiln used for melting glass, up to 880 C for 60min. I have plaster cast mold...

11 March 2018 5,326 1 View

Acarina from pigeon nest ?

The acari were found in the nest of feral pigeons (Columba livia domestica) collected in the centre of Ljubljana, Slovenia. The pigeons build their nest in the ceiling of the balcony above the top...

15 January 2018 394 4 View

How do ventilated facade affect a building.

i need to know both the positive and negative effect a ventilated facade

02 March 2016 998 5 View

Are there annually repeated studies on the deployment and management of IT?

I have conducted an annual survey for the Finnish Data Processing Association since 2009 (6 times so far). The survey is primarily addressed to IT and business managers of organizations with more...

05 December 2014 7,104 11 View

What can we do about suicide (self-murder)? Do we "treat" the problem or do we offer talk? And should we coerce folks in such existential crises?

The role of coercion of course is very fundamental to psychiatry and perhaps is the only continuously related tool it has used even though the literature is clear, coercion is not effective. I am...

14 November 2013 607 12 View

Why modelling the development of societies fails?

It would be nice to get reading succestions addressing the topic why modelling societies and their dynamic developments may fail. What are the challenges and pitfalls when one attempts to create...

01 January 1970 6,752 3 View

Bayesian inference and maximum likelihood for phylogenetic tree

i tried to build a tree between bayesian inference and maximum likelihood algorithm using the same sequence but i got the different result. i reconstructed 5 homolog sequences with no polymorphic...

01 January 1970 6,596 2 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

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

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Why my colony PCR results of my recombinant bacterial not showing any results?

I am performing ligation of the plasmid and a target gene. The steps I have taken are: 1. Double digestion of the plasmid and target gene 2. Ligation of the plasmid with the target gene 3....

05 August 2024 2,570 3 View

What is the acceptable p-value cutoff for GO enrichment analysis ?

I have an RNA-seq data that I have analysed using Limma-voom and have extracted the gene IDs, log2FC and the p-values. At p value < 0.05, I have over 10,000 DEGs, however, when I run the GO...

31 July 2024 225 2 View

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

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View

Are these cassettes suitable for expressing PETase mutant in E. coli?

I created two potential gene expression cassettes (constitutive and inducible) for expression of a mutant PETase gene on PeptiCloud using the version tree feature, which allows users to create...

28 July 2024 7,559 1 View

Optimal siRNA Volume for Complexation with Liposomes in a 2.5 mL Solution with 10 mg/mL Lipid Concentration?

How much volume of siRNA can I add to 2.5 mL of liposomes with a total lipid concentration of 10 mg/mL?

27 July 2024 6,920 1 View

If my gene of interest has high GC content can it be problematic in sequencing? What kind of error is expected with GC rich gene sequences??

Gene sequencing related trouble shooting

25 July 2024 4,149 2 View

Why my negative control siRNA is decreasing the target gene's expression?

Hi Everyone, I'm using an siRNA kit to knock down a target gene. The kit guarantees that the negative control doesn't target any sequence in mouse genome, and when I use BLAST I don't find any...

23 July 2024 2,673 6 View

Mass spectra averaging algorithm?

I am now developing a python module for ms2 database searching, would like to realize a function that similar to what Xcalibur did, choose multiple mass spectra and get an averaged spectra. But...

22 July 2024 3,975 1 View

Ayoob Radhi

You can use amino acid sequence alignment

Kiran Dindhoria

You have to concatenate all target genes and then construct the phylogenetic tree. There are many software available for doing this like MEGAX, RAxML etc.

Francisco J. Enguita

Hi there

If you want to align and produce a phylogenetic tree, starting from a multi FASTA file containing all the sequences (genes or proteins), you have very good options. I routinely used the web site www.phylogeny.fr where you will directly get the .

If you want to further manipulate the tree you can use additional software such as Dendroscope.

Hope it helps. Best

Paco