I am new to bioinformatics and was wondering what genome viewer program users of site utilize in order to visualize their reads.
I'm currently using IGV but it is very limited in it's ability to find motifs in a sequence.
I have reads that map to 45S, a gene that codes for human rRNA.
Ideally, I would want a program that could do each of the following for the most highly abundant reads:
- Analyze GC content
- Determine secondary structure
- Common sequence motifs among reads
- protein binding domains (using the RNA sequences, determine proteins that have a high binding affinity)
- sequence similarity between RNA reads (align reads with high coverage to one another)