Tools to translate from proteome to genome and understand genomic data

Question

[giammafer]

Hello everybody, I have two questions:

Which free software allow to translate proteomics data into genomic data?

Could you suggest the top five free software/platforms that allow to explore and understand genomic data?

Thank you all for your kind help.

[lieven.sterck]

Your question(s) are very vague. Can you add some more detail? (will only help to get more meaningful answers) eg. what do you want to explore the genomic data for?

[giammafer]

Yes, I realized that I have been too much vague about my purpose.

The scope of my analysis is to take a PLGS output file that contains a human proteome. Then, I would like to map back the proteins on the genome.

In general, I am expecting to fetch the proteins' id. Subsequently, I think that I need to translate back the genes into the mRNA. Finally, to visualize on a genome browser, where they are located.

I was wondering if exist a pipeline for such kind of analysis.

In this starting phase of the project, I am trying to divide the problem into its main steps and figure out which online tools are already available to perform each step of this analysis.

Answer 1

[lieven.sterck]

thanks for the clarification.

You could consider to map the proteins directly? There a several tools around that 'map' proteins (and with map I don't mean blast, but really do splice-aware alignment of the proteins). Eg. GenomeThreader, GeneWise, ...

real translation of proteins back to their mRNA is in most cases nearly impossible. You could look up the proteinIDs and query the corresponding CDS/mRNA sequence and align those (as you propose) but depending on the accuracy you need it will be a needless detour compared to directly mapping the proteins. (key is here to use splice-aware protein aligner)

[giammafer]

Yes, I think that for the purpose of my project I can start from proteins going straight to the genome.

I will try your suggestion.

Thank you very much.