I´m starting to work with different mRNA sequences. I would like to know what software you recommend to analyze, among other things, the percentage of each nucleotide in the sequence.
can be set to word size =1 one to get base composition or word size =2 to see the dinucleotide bias (for example CG is selected against due to methylation).
It is often useful to look at "GC skew" in bacterial genomes, over a window of some size, because in a GC skew plot the gene orientation is often highly correlated with the skew. See the attached plot for example. The overall base composition does not show this level of detail.
There are many software packages or web sites that will do composition analysis. You can also do it in Microsoft Word (enter your sequence, sort by letter and do character count for each)