(not sure if this is a question, it's more of a poll)
I would like to know what is the next step in a common genome analysis after the following ones:
Sequencing genome
Assembling genome
Annotating genetic elements in the genome assembly
Aligning genome against other species in the clade in a multiple genome-wide alignment
Find interesting information in the alignments
I would like to know what are the common questions people ask after having done the genome-wide alignments and what tools are commonly used to answer those questions.
It seems that this question is posed backward. People should start with a research question and hypothesis then they pick the analysis to match the goals.
Perhaps you are asking about the various applications of sequencing.
I am writing this mainly since this is a pet peeve of mine. Doing this backwards, sequence first then run analyses to find interesting stuff is a surefire way to discover all kinds of spurious results. Unfortunately this is an endemic problem for bioinformatics in general. In the current state of affairs we are unable to properly asses the biases introduced by data preparation and instrumentation and most people are also ill prepared when it comes to properly account for multiple testing corrections.
Just fishing for interesting results leads to mountains of irreproducible results - a lot of which actually gets published.
Usually one sequences a new species because of some interesting aspects of its biology. In that sense, Istvan comment is very appropriate, but let me give you a few very quick examples of analyses that have been done with some vertebrate genomes.
In the analysis of the turkey genome, one of the questions was to address how much conserved sequence there is in avian genomes. These genomes being significantly shorter than mammalian ones, it wasn't clear if they contained the same amount or the same percentage of conserved sequence. Earlier, the zebra finch (the bird and not zebrafish the fish) was sequenced to discover genes involved in vocalization. One of the main points in the analysis not the gorilla genome was to look at the incomplete lineage sorting among human, chimpanzee and gorilla. With the sequence of the first teleost genome, one could look at the additional round of whole-genome duplication that happened in that lineage.
Those are a few examples of what people have been looking for in the new genome sequences. Again, there is no stereotypical analysis, as this depends very much on the biology and evolution of the species.
