What are some (bioinformatic) methods to characterize potentially novel gene transcripts?
I am working with a few novel transcripts of genes- before I confirm their existence experimentally, I would like to perform some bioinformatic analysis. I have already considered coding potential, protein domain prediction, transcription factor binding sites, sequence homology, and RNA secondary structure (still a little unsure how to use this one). These transcripts were discovered using RNA-Seq. Are there any other elements of genes/confirmed transcripts that I should look for in the sequence of my transcripts and corresponding softwares? (I can find the software myself if necessary, but I have run out of characteristics to search for). I would like to characterize these transcripts structurally and functionally as completely as possible, including potential protein function, mRNA degradation, etc - some new features for what to look into would be appreciated.
Some additional things worth checking out with your RNA:
Alternative splicing of your novel transcripts. Alternative splicing is a common form of producing variation in proteins. This can usually be seen at the RNA level. In projects where I have studied alternative splicing, I generally like the program rMATS however this can also be completed with the Ballgown suite.
Potential protein function. This entirely depends on how well assembled and annotated the genome of your organism is. If your organism's genome is poorly annotated, Blast2GO is a GUI program you can download. This will take care of PFAM, KEGG, BLAST, and GO Term searches for you and will combine them nicely in a single file for you. These searches together are helpful in identifying the possible function of genes of interest.
If you'd like additional consultation on this feel free to reach out about tutoring availability.