SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Polymorphism in de novo assembled transcriptomes SJLH Bioinformatics 0 03-18-2013 07:47 AM
Comparing two proteomes/genomes! pulikoti Bioinformatics 3 10-09-2012 06:52 AM
How to calculate RPKM of de novo assembled sequences zinky De novo discovery 4 06-08-2012 12:06 AM
overlap between multiple de novo assembled samples boetsie Bioinformatics 1 12-13-2011 08:08 AM
comparing results from two different reference genomes BAJ Bioinformatics 2 02-24-2009 07:38 AM

Reply
 
Thread Tools
Old 02-17-2014, 04:40 AM   #1
calbertovj
Junior Member
 
Location: Wageningen

Join Date: Feb 2014
Posts: 1
Default Comparing two de-novo assembled genomes

Hi all,

I would like to compare two fungal genomes that have been sequenced and assembled de novo. These genome are different isolates from the same species but have different genome sizes (33.4Mb and 37Mb). They are haploid. I have predicted the genes for each genome using Maker. I would like to compare these genomes in several ways:

- List of genes that are unique to both isolates and list of genes that are common.
- Detect Structural variation: gene duplication, rearrangement, etc.
- Any other interesting feature ??

Any advise would be highly appreciated since my bioinformatics skills are low. Which software can I use??
calbertovj is offline   Reply With Quote
Old 02-18-2014, 05:08 AM   #2
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

Comparing gene names is very simple: use comm command.
Structural variation: map reads back to the genomes and use VariationHunter, SVDetect or other program from this list.
TiborNagy is offline   Reply With Quote
Reply

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 06:54 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO