SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How I find not assembly read in a reference assembly??? matiasfreired Bioinformatics 1 04-05-2012 12:13 PM
alternate path to install 454 software? sjmillerAZ 454 Pyrosequencing 4 11-28-2011 08:16 PM
Alternate contig scaffoldings with ABySS RLB_84 De novo discovery 0 10-13-2011 04:04 PM
de novo assembly vs. reference assembly fadista General 3 02-15-2011 11:11 PM
what does it mean a hit to alternate assembly?? litali Bioinformatics 0 07-19-2010 08:42 AM

Reply
 
Thread Tools
Old 10-03-2010, 02:28 AM   #1
litali
Member
 
Location: us

Join Date: Jul 2010
Posts: 78
Default alternate assembly

Hi all,
I wanted to ask what is alternate assembly in blast and how I should treat it. I mean that I find structural differences when I am doing a mapping project, but then, when I check it in blast, I find that it firs perfectly alternate assembly, so it is not a real variation? how can I avoid this situation?
THANKS!!!
litali is offline   Reply With Quote
Old 10-03-2010, 06:28 PM   #2
Jon_Keats
Senior Member
 
Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279
Default

The alternate assembly or often assemblies are just that alternate build of your given genome from different individuals. The simple solution is to first pick the reference genome you want to use then in blast settings select to blast just this reference so you don't get hits from all the possible assemblies. Unfortunately, Watson and Venter are not identical twins so even their builds are not identical...go figure
Jon_Keats is offline   Reply With Quote
Old 10-04-2010, 12:45 PM   #3
litali
Member
 
Location: us

Join Date: Jul 2010
Posts: 78
Default alternate assembly

Thank you. Yes, I understand that there might be assemblies from different people and I can set the settings in blast not to see it, but the question is not whether I see it or not but whether the structural difference I found when mapping to the reference genome is a mutation, and if I understand correctly, if there is an alternate assembly like this, this is not a real mutation?
litali is offline   Reply With Quote
Old 10-04-2010, 01:03 PM   #4
Jon_Keats
Senior Member
 
Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279
Default

Quote:
Originally Posted by litali View Post
Hi all,
I wanted to ask what is alternate assembly in blast and how I should treat it. I mean that I find structural differences when I am doing a mapping project, but then, when I check it in blast, I find that it firs perfectly alternate assembly, so it is not a real variation? how can I avoid this situation?
THANKS!!!
True versus false variation is dependent on your research question. If you are looking for novel disease causing structural variations you can use blast as you are doing to filter out things in the other assemblies or use some of the various databases to exclude known variants in other datasets. But if you are looking of misrepresented variants you are talking more about annotation and counting versus filtering. But the short answer is if the variant is in another assembly it is not a real/novel variant. So you should filter your reference genome variant list against a list of known variants which are available in a number of databases
Jon_Keats 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 01:33 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO