I have 2 complete genomes sequences (Annotated and Assembled)
DNA Sequence and AA sequence too.
Thanks.
You are going to have to be more specific than that. What kind of analysis are you interested in? How big are the genomes? If you just want a bioinformatic software that could solve this problem, you should look into learning R/bioconductor since it if often used to generate nice figures. If your genomes are large, you might be off writing custom scripts in python/C/etc to get the numbers/data you need and then visualize it with different software.
Thanks Ying wu,
for exemple:
im looking for C/G content of each genome, similarity of this genomes, number of duplicates sequences, Frequency x Position of Sequence Ends, Poly A/T tails etc...
I will try to use R/bioconductor...
My sequence is not so big it's a prokaryotic (Rhizobium).
This would be a lot of work but you should look into BSgenome package of bioconductor (http://www.bioconductor.org/packages/release/bioc/html/BSgenome.html) as well as Biostrings (http://www.bioconductor.org/packages/release/bioc/html/Biostrings.html) these two packages can probably do the analysis you are looking for but the learning curve might be pretty steep. You can find some guides available on the bioconductor website to help you along.
Hi Arthur Siqueira, My professor has developed a great software called "DAMBE" for comparative genomics. It will be really helpful for you. If you need more help in using it. Do let me know so that I can help you.
For the protein sequences in the gemomes that may be aligned, you may use the toolbox DeltaProt. Read more about it here:
http://www.biomedcentral.com/1471-2105/11/573/
You can explain me in detail, so that I can suggest you which are functions to be used in that tool.
What tool Ramanandan? There are so many listed here. Thanks
Now i'm using RAST, i've uploaded my sequences there...I'll try to use DAMBE if will be necessary.
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