Question: Best Genome Viewer Program
0
gravatar for ganurudh
2.3 years ago by
ganurudh0
ganurudh0 wrote:

Hello all,

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)

Thanks!

rna reads sequence motifs • 678 views
ADD COMMENTlink written 2.3 years ago by ganurudh0
2

If you need/want a program to do all those things then it does not remain a genome viewer any longer, does it?

There are other programs do all those things. IGV in some cases is able to import the results from those programs and allow you to view them, which is its primary function.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax58k

Hello genomax2,

Thanks for your input!

I would want to export these sequences of interest from the genome viewer to perform the tasks listed in my previous post.

Do you know any programs that do the tasks listed above?

Thanks

ADD REPLYlink written 2.3 years ago by ganurudh0
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