SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Polymorphic microsatellites from whole genome sequencing akashrestha General 2 10-05-2013 08:32 PM
How to query microsatellites in a set of data NGS_New_User Bioinformatics 1 05-24-2013 07:43 AM
Microsatellites development with Next G. seq + Illumina transcriptome analysis Alexander Tchourbanov Bioinformatics 2 10-07-2012 06:42 PM
sequencing microsatellites koen de gelas 454 Pyrosequencing 1 08-29-2012 04:50 PM
Paternal testing microsatellites johnadam33 Genomic Resequencing 1 06-26-2012 02:03 PM

Reply
 
Thread Tools
Old 05-18-2014, 02:06 AM   #1
Bara'a Al-Hammad
Member
 
Location: Amman-Jordan

Join Date: Feb 2014
Posts: 16
Default Detecting plants Microsatellites

Hello ...

I'm working on a thesis in bioinformatics , and I need to accomplish the following task using BLAST plant EST database .

Given 10 different plant species , I need to test the hypothesis assumes that genes containing SSRs are one of the sources that defect existing or generate new genes , leading to form pseudo-genes or non-translated expressed genes that could form microRNAs or form new genes , through the following procedure :

1.first by matching the left strand of flanking region of a given sequence to the left strand of flanking region of another different one , and the left strand of flanking region of one sequence to the right reverse complimentary strand of flanking region for the second sequence .

2.Then ; comparing the right strand of flanking region of a given sequence to the right strand of flanking region of another different one , and the right strand of flanking region of one sequence to the left reverse complimentary strand of flanking region for the second sequence .

The results of such comparisons are considered candidate genes that follow the hypothesis of 50% minimum difference between similarities of comparison phases , which will be further examined to detect their functional change through the evolutionary path of those 10 species on both levels of nucleotide sequences and protein sequences (for accuracy purposes ).


How can I perform this task and get the most accurate results out of it ?

I will be very grateful and thankful if you could guide me with some detailed steps , as I'm kind of lost here and don't know where to start from .
Bara'a Al-Hammad is offline   Reply With Quote
Reply

Tags
microsatellites, plants

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:27 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO