The past few years has seen an increase in sequencing of whole genomes. Though raw data is available nowadays, deriving functional relationships at the genome level have just few tools. For example , at the gene level one can do a BLAST search , Multiple sequence alignment or phylogeny etc. But what are functional relationships available or possible when working with whole genomes?
Please mention some tools (or) algorithms (or) or mathematical methods that are attempted which keep whole genomes in their scope!!!
It depends on what you want to with whole genomes. Some Linux-based utilities are developed. Also CLC genomic workbench is possible to use for assemling, BLAST iside genome and many other things.
What organisms are you researching? There is a huge difference in approach between prokarytoic and eukaryotic organisms, starting with the size!
Thanks everyone for your reply.
I am trying to resolve functionality between prokaryotic genomes. Yes , Size does matter. Are there any nonlinear or pattern searching methods that can differentiate prokaryotes for particular features.
For example , Phylogeny to start with...
it is done at gene level using PHYLIP ..... I did not find methods which can construct a phylogenetic tree at whole genome level....
Phylogenetics for whole genome data can be done by aligning orthologous genes and using a multi-gene approach, either concatentation with partitions, or Bayesian co-estimation of gene and species trees. I recommend the recent Nature paper on bird phylogenomics. There are also alignment free approaches based on k-mer content etc. What data do you have? What is your biological question?
I have to rely on prokaryotic genome databases linked to NCBI.
As you said , I am talking about alignment free approaches. I could send a paper which developed chaos game representation for handling genomes and they tested it on a dataset. They declare that their results are reliable!!
This may not be helpful but when I had to analyze my whole genome data, I went through whole genome analysis publications of similar organisms to find the "standard" way of going about the analysis.
When you say functional relationship, I assume you are asking about the role of the predicted proteome based on the genome? There are, for example, at least 10 tools available for prediction of secreted proteins. Among them, you will find prediction for transmembrane proteins, mitochondrial proteins, etc. So depending on what your focus is, there are probably a few tools that will help you find out what you want to know. This is different approach than just comparing genome sequence.
Try Phylosift - analyses multiple loci simultaneously from genome data.
We have recently developed a pipeline in our software BioNumerics that will allow for the detection of all known coding loci of a prokaryotic organism and a subsequent clustering based on all these alleles. Another approach that is possible, is aligning all genomes against a well chosen reference, performing a snp search and then clustering based on these snps.
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