SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
[PERL] Compare two sequences from fasta file frenchcookie Bioinformatics 3 12-17-2012 08:59 AM
Sequence transposon flanking region Akira Sample Prep / Library Generation 8 03-18-2012 07:53 AM
Vector trimming: are flanking sequences sufficient? sulicon Bioinformatics 1 09-20-2010 08:02 AM
Compare SNPs bair Bioinformatics 5 01-27-2010 03:38 AM

Reply
 
Thread Tools
Old 04-11-2013, 10:52 AM   #1
cascoamarillo
Senior Member
 
Location: MA

Join Date: Oct 2010
Posts: 160
Default How to compare sequences and flanking regions

Hi everyone,
Sorry, but here comes the stupid question of the week: I want to look for similar sequences in a draft genome, and choose those with different flaking (at 3' and 5') regions (cos the genome has contig duplications all along the sequence).
So let's say, I have a group of similar seqs (ca. 200bp) and I want to check their 3' and 5' 50bp surrounds. In a total ~300 bp seqs database, is there a way to say to blast (or maybe other program) that I need to pick up the similar sequences in position 50-250 but with differences at 1-50 and 250-300?

Thanks
cascoamarillo 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 06:35 PM.


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