SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Question about Cufflinks and reference annotations mhayes Bioinformatics 1 03-23-2015 06:40 PM
annotations intervals problem roshanbernard Bioinformatics 1 01-18-2012 05:28 PM
Annotations of rRNA genes steven General 0 09-08-2010 06:31 AM
Annotations using GS Mpper pmishra1982 Bioinformatics 4 02-24-2010 10:13 AM
comparing sequences and mapping annotations? gaster Bioinformatics 0 07-06-2009 01:33 PM

Reply
 
Thread Tools
Old 01-18-2012, 05:39 PM   #1
roshanbernard
Member
 
Location: South Korea

Join Date: Feb 2011
Posts: 31
Default annotations

I use annotations pipelines like RAST or NCBI or JGI to get the bacterial genome annotation...


however, if there is any mutation among the promoter of the gene, does the servers annotated them or just disregards it..

anyone have idea about this...??
roshanbernard is offline   Reply With Quote
Old 01-18-2012, 10:58 PM   #2
maasha
Senior Member
 
Location: Denmark

Join Date: Apr 2009
Posts: 153
Default

I am pretty sure RAST doesn't annotate such. Try the RAST mailing list - they are most helpful.
maasha is offline   Reply With Quote
Old 01-18-2012, 11:14 PM   #3
roshanbernard
Member
 
Location: South Korea

Join Date: Feb 2011
Posts: 31
Default

Hi,

i got the reply from RAST team///i am pasting the reply below....


Unfortunately, the only type of promoter sites RAST can recognize
are Ribosomal Binding Sites. RAST cannot yet recognize any type of promoter site
other than the RBS.

Hence, mutations in the upstream region will not have any impact on RAST's
gene-calls or annotations unless they weaken the RBS site so much
that the correct START site fails to be found.
roshanbernard is offline   Reply With Quote
Old 01-18-2012, 11:14 PM   #4
roshanbernard
Member
 
Location: South Korea

Join Date: Feb 2011
Posts: 31
Default

and thanks a lot masha for ur reply..:-)..
roshanbernard 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 04:08 AM.


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