Question: Some examples of Intron aware aligner?
0
gravatar for Kenny
12 months ago by
Kenny10
New York
Kenny10 wrote:

Hi all,

I would like to do gene annotation on my genome assembly. My PI wants me to use intron aware aligner and I found the following programs:

Apollo (http://genomearchitect.github.io/)

Rail-RNA (http://docs.rail.bio/)

Have someone used the above programs before? Do you have any other suggestions?

I am new in this field, any help will be appreciated!

Kenny

alignment • 370 views
ADD COMMENTlink modified 12 months ago by Puli Chandramouli Reddy150 • written 12 months ago by Kenny10

It's unclear which data you exactly have and what you aim to obtain, please elaborate.

ADD REPLYlink written 12 months ago by WouterDeCoster35k

I have a scaffold genome and transcriptome of an organism. I have blast the transcriptome against the genome. When I checked the blast output, for example, one transcript appears in different scaffolds. Another example, one transcript appear in the same scaffold but there are gaps. I guess there might be an intron there. Therefore, I would like to visualize the genome and transcriptome to find out.

Hope I make this a bit clear.

ADD REPLYlink written 12 months ago by Kenny10
1

If you are only looking to align a transcriptome against a genome/scaffold then take a look at GMAP.

ADD REPLYlink written 12 months ago by genomax59k
1
gravatar for Puli Chandramouli Reddy
12 months ago by
Pune, India
Puli Chandramouli Reddy150 wrote:

Hi,

If you want to map or align transcripts to genome then you can use Exonerate or NUCMER or BLAT.

ADD COMMENTlink written 12 months ago by Puli Chandramouli Reddy150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1276 users visited in the last hour