Where Should I Start From ?

Question

[Bara'a]

Hi all . I'm new to this field as I'm working on my thesis , and I'm kind of lost here .

My main objective is to prove the hypothesis assumes that Microsatellites regions in plants genomes could be one of the forces that lead to defect existing or generate new genes or lead to form pseudo-genes or non-translated expressed genes as they are considered hotspots for homologous and non-homologous crossing over .

Also , I need to detect the changes in the functional annotation of genes , and the changes that might occur in the same family using synteny analysis and pairwise alignment by evaluating the resemblance degree between the left sides of Microsatellites regions in multiple genes , and the right ones as well .

My supervisor directed me to use the NCBI BLAST+ and BioEdit software to perform some of the main objectives , but when I get into it them I was confused and didn't know what to do .

Any valuable comments and help would be appreciated .

Answer 1

[Sean Davis]

I hate to be patronizing, but I would suggest going back to your advisor to:

1. clarify expectations and priorities
2. establish an informal training program for you
3. define some minimal resources to help you complete your tasks (papers to read, other postdocs or students to work with, local bioinformatics experts)
4. agree to meet regularly to present your incremental results and adjust your priorities

I did not address your question directly. I think once you spend some time sorting out a little clearer plan, it will be easier to ask questions that can be easily answered in this electronic format.

[Bara'a]

Sean Davis ... I do have some resources and data sets , and I do know the objectives very well but since I'm new to the field I don't know yet much knowledge to start performing the goals .

As I'm a computer science student , there have to be some contribution of programming to accomplish the tasks ... so , after reading your reply and stating clear and precise steps , my question would be : What tools can I use to detect the existence of Microsatellites in plants genomes ?

Thanks in advance .

[Sean Davis]

Nice reply! I'd suggest asking this as a new question and be sure to include information about the types of data you are starting with in addition to your question. Be as specific as possible.

[Bara'a]

Well thanks ... I will !!