It seems the package HDMD can help me, but again, I need to 'compare' different sequences to have en entropy score. Reverse Complement Reverse Complement converts a DNA sequence into its reverse, complement, or reverse-complement counterpart.

I heard that shannon's entropy can help me in that, but I am actually not very sure.ġ) it seems it works fine to find motifs, to find what's possibly common when comparing sequences ( ) and I think I quite understand how it is calculated.Ģ) I have found some formulas and calculator to calculate a general entropy ( ) that is interesting and it may help me.ģ) I was, however, thinking that maybe I could calculate an entropy factor for a given sequence regarding repeated motifs it may have ( like in this paper )Ĥ) finally, but I think I can't find it back, I would have been in search for a 'by position' entropy, that would show a decrease of complexity in some parts of my sequences. I'd like to show it with a 4 letters genome, and a 3 letters genome (bisulfite converted). In the sequence below, there is 67 similarity (6/9 nucleotides), with total 3 total mismatches (Hamming distance). Each sequence is compared nucleotide by nucleotide, and matches are highlighted and designated with bar symbols. I would like to explain by this that some mapping issues can come from there. Two or more DNA or protein sequences can be compared for similarity at the local and global level.

It is the volume of the starting solution to add to the dilution.I am trying to propose a way to show that a given sequence, given to another one is less/more complex. Genome-to-Genome Distance Calculator (GGDC). You can use DNA Calculator to: Calculate basic physical and chemical parameters of a nucleic acid molecule. This converter is used to estimate the size of the gene by the protein size, and vice versa.

Solving for V 1 creates the following equation: DNA and Sequencing Genomics and Transcriptomics Biodiversity Informatics.

V 1 = volume to add to dilution (unknown).

Determine the dilution needed using C 1V 1 = C 2V 2 People with a solid understanding of the relationship between the units of ng/μl and nM can skip some steps, but the most comprehensive set of step between these two units is ng/μl > g/μl > moles/μl> moles/L = M > nMĢ. The RBS Calculator is embedded into Genome.

1 mole of nucleotide base pairs = 660 g The RBS Calculator is used by GenScript to synthesize DNA sequences with custom-designed ribosome binding sites.

Paste sequence two (in raw sequence or FASTA format) into the text area below. Paste sequence one (in raw sequence or FASTA format) into the text area below.

Use Pairwise Align DNA to look for conserved sequence regions. Concentration in ng/μl (starting point) Pairwise Align DNA accepts two DNA sequences and determines the optimal global alignment.The conversions factor and other inputs needed to perform these conversions are: The inverse of the molecular weight is the number of moles of template present in one gram of material. This makes the formula weight * of the base pairs in the double stranded DNA 660 g. This concentration in nM is used as the starting concentration for a dilution step to obtain a solution at the target concentrationĪssumptions: These calculations assume the sample is double stranded DNA and that the average mass of a pair of nucleotide bases is 660 Daltons (Da).The sample concentration is converted from ng/μl to nM.There are two steps involved in this calculation:

Dna sequence calculator