Detect polymorphic SSRs between two assemblies

[Mithril]

Hello all,
I have generated two assemblies from two separate genotypes. Is there a tool to search for polymorphic SSRs between these two assemblies?

[adaptivegenome]

Can you explain a little more exactly what you have done what data you have?

[Mithril]

Well, I got 454 reads from 2 seperate genotypes. They were assembled and annotated. Now I want to generate SSRs that are polymorphic between the two assemblies. MISA is generally used to detect SSRs but i want to go one step ahead and try to find SSRs that vary in their repeat number between sequences that are the same in the two assemblies.
Is there any way to go about this excercise?

[adaptivegenome]

Well, I got 454 reads from 2 seperate genotypes. They were assembled and annotated. Now I want to generate SSRs that are polymorphic between the two assemblies. MISA is generally used to detect SSRs but i want to go one step ahead and try to find SSRs that vary in their repeat number between sequences that are the same in the two assemblies.
Is there any way to go about this excercise?

First I do recommend TRF for finding repeats. I think this works best. Second there is not an automated tool that I know of that will perform an alignment between the two sequences and compare repeats in them. So you would have to find repeats in one sequence and then align the sequences and write a script to measure the size of the repeats in the other sequence.

We have a tool for finding repeats in nextgen alignments but my guess is that it would perform poorly using 454 data...

[Mithril]

Oww.. Alright I will run the data through TRF, would it be possible for you to link me to the tool that you are talking about?

[adaptivegenome]

Oww.. Alright I will run the data through TRF, would it be possible for you to link me to the tool that you are talking about?

Here you go...

http://tandem.bu.edu/trf/trf.html

Something to consider, you probably want to use TRF to find repeats in both sequences as if you only use 1 sequence you could introduce ascertainment bias.

Anyways good luck and post again if you have trouble.

Also depending on the species, UCSC usually might have a TRF output already online. But the code is incredibly easy to run.

[Mithril]

Thank you for the TRF link,

In an earlier post you had mentioned that you did have a tool to find reads in nextgen alignment but may not work for 454, would it be possible for me to use the tool too?

Thank you for your help!!

[adaptivegenome]

Thank you for the TRF link,

In an earlier post you had mentioned that you did have a tool to find reads in nextgen alignment but may not work for 454, would it be possible for me to use the tool too?

Thank you for your help!!

We are in the process of preparing a manuscript for publication but would be happy to share our code early. Just send me PM and we can discuss offline.

[JamesH]

Are you trying to find polymorphic markers so that you can design primers and screen them in a bunch of individuals? If so this is what you're after:

http://gsite.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html

You just give it all your unassembled sequences as a single fasta file, it will remove reads that look like transposons (based on similarity), identify microsatellites, design primers using primer3 and then report which ones are polymorphic in the output, along with a bunch of other useful info! Works great on 454, and will build consensus sequences as well.