Good day house. I am working on Molecular Evolution and Phylogenetics of some organisms. Before conducting my Synonymous to Non Synonymous substitutions after Sanger Sequencing, I would need to get various statistics from my DNA sequence. Asides these:
1. Base Composition
2. GC content
3. Word pattern
4. Over represented and under represented words
What are the other DNA Sequence statistics that could/might bring out something from the sequence with respect to analysis?
It depends a bit on what type of organisms you are studying: bacteria, virus, plant, animal, etc. For some organisms it is interesting to look at CpG dinucleotide because this gets methylated and then mutates to ApG or CpT so genomes with meythylation are very much depleted in CpG dinucleotide content. For bacteria it can be interesting to look for transposons and other mobile elements. For bacterial genomes the "GC skew" can be useful in identifying genes and direction of replication.
It can be very informative to do most of these analyses in a sliding window, rather than over the entire sequence. I am attaching a figure made using the gwBrowser genome browser which plots many DNA attributes or statistics as rings. In the pink vs cyan inner ring you see the GCskew and how it correlates with the gene orientation on the plasmid (Blue vs Red on the outermost ring). The dogma is that GC skew is due to direction of replication and not direction of transcription. But my studies of Clostridia make me question the dogma.
It depends a bit on what type of organisms you are studying: bacteria, virus, plant, animal, etc. For some organisms it is interesting to look at CpG dinucleotide because this gets methylated and then mutates to ApG or CpT so genomes with meythylation are very much depleted in CpG dinucleotide content. For bacteria it can be interesting to look for transposons and other mobile elements. For bacterial genomes the "GC skew" can be useful in identifying genes and direction of replication.
It can be very informative to do most of these analyses in a sliding window, rather than over the entire sequence. I am attaching a figure made using the gwBrowser genome browser which plots many DNA attributes or statistics as rings. In the pink vs cyan inner ring you see the GCskew and how it correlates with the gene orientation on the plasmid (Blue vs Red on the outermost ring). The dogma is that GC skew is due to direction of replication and not direction of transcription. But my studies of Clostridia make me question the dogma.
Brian Thomas Foley Thanks very much for your answer. I really appreciate it. I am actually working on haemoparasites in the malaria parasites' family - Plasmodium, Babesia, Eimeria (Apicomplexans).
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