Question: Detecting Plants Microsatellites
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gravatar for Bara'a
5.5 years ago by
Bara'a230
Amman - Jordan
Bara'a230 wrote:

Hi all ...

I'm working on a task in plants bioinformatics to prove the hypothesis assumes that genes containing SSRs are one of the sources that defect existing or generate new genes, and I've been wondering what tools can I use to perform a plant Microsatellite detection ?

and what type of inputs/information  do I need to use them ?

Thanks in advance

 

microsatellites plants • 1.3k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 5.5 years ago by Bara'a230
1
gravatar for Prakki Rama
5.5 years ago by
Prakki Rama2.3k
Singapore
Prakki Rama2.3k wrote:

You can try running censor to find the microsatellite information. The results are written to output file with .map extension. Since you are in need to check only the plant microsatellites, you can use -lib by changing it to plnrep.ref.

EDIT: -lib here means library you wanted to search for. The plant repeat database is searched by censor, if you put -lib plnrep.ref in your censor command. (Default running of censor will search for all the databases including humans and other organisms which you did not intend.) But, I honestly do not know if the microsatellites are specific to an organism as pgibas pointed.

 

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Prakki Rama2.3k
Thank you for your reply, but I found it a little vague for a begginner like me!! Would you please explain it more, and I will be very grateful :)
ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Bara'a230
1

check my edit.

ADD REPLYlink written 5.5 years ago by Prakki Rama2.3k

 Thank you; this is a way better answer :)

Regarding your note about whether Microsatellites are organism specific; from my humble knowledge in this field I can say that they are abundant in all organisms but differs in structure and functionality.

Any repeat expert to approve this information?!

ADD REPLYlink written 5.5 years ago by Bara'a230
1

May be try posting it as separate question instead of asking in comment. You may get the clear answer from users.

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Prakki Rama2.3k
1
gravatar for PoGibas
5.5 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

Why not Tandem repeat finder? I guess it is one of the oldest and most used tool to identify tandemly repeated sequences (including microsatellites). I use it a lot and don't need anything else.  

Input is sequences in fasta format. You can use one sequence or fasta file with multiple sequences; you can run it using genome as input or seperate gene sequences. Output is informative and easy to parse. There are many options to play around. For example, "maximum period size". If it is "1", then you'll get only AAAAAA; if it is "2", then you'll get AAAAA and CGCGCGC.

You can download your own copy or use it online.  

Good luck with your hypothesis! 

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by PoGibas4.8k

True. But, I think TRF is a Denovo repeat finder. Even if TRF finds repeats, the user should still needs to rely on existing database to verify if it is plant specific repeat or not.

 

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Prakki Rama2.3k

Are microsatellites so specific?  I mean, long satellites can be species specific, but short satellites (like ACAC..) should be more global thing. Isn't it? I am just guessing.  

Nonetheless, if OP is just starting, TRF might be a good start to play around with sequences and bioinformatic data. 

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by PoGibas4.8k

I am also not quite sure about that. Would like to hear, if there are some repeat experts in the forum. 

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Prakki Rama2.3k

Thanks a lot Pgibas... I appreciate your reply , can't thank you enough .

But; what about the note Prakki Rama mentioned ?

Can I rely on TRF alone to get started with my data analysis or not ? if so; would any repeat expert in the forum guide me to the right direction please ?

Thanks in advance :)

ADD REPLYlink written 5.5 years ago by Bara'a230
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