SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Miseq custom primer design, primer linker Cyrus Taheri Illumina/Solexa 1 04-21-2015 05:25 PM
Illumina Custom Sequencing Primer tgyuris Illumina/Solexa 4 09-16-2014 07:43 AM
Custom primer failed kal33na Illumina/Solexa 1 04-22-2013 01:39 PM
50+% of my HiSEQ reads are 3' primer (custom primer used) ZAAB Sample Prep / Library Generation 3 02-06-2012 11:00 AM
custom primer menglv Illumina/Solexa 3 01-18-2011 01:01 PM

Reply
 
Thread Tools
Old 10-06-2015, 08:46 AM   #1
sam12
Junior Member
 
Location: United States

Join Date: Jun 2015
Posts: 1
Default blastn help for primer alignment to custom db

Hello!

I am trying to find primer pairs that will amplify across 6 individuals of the same taxa. I have forward and reverse primers(<30bp each) for each individual that were generated by QDD, and am now trying to blast the primers from each individual to the microsatellite sequences(msat + flanking regions) from the other 5 (ex. primers from A blasted to msat sequences from B,C,D,E,F). The goal is to find which primers will align in all 6 individuals so that we can order the primers and test if they amplify in the lab.

This is the blast command I'm using right now. I want the results to be only alignments that span 100% of the query sequence. Really, a global query:local database alignment.

>>blastn -task blastn-short -qcov_hsp_perc 100 -perc_identity 100 -ungapped -num_threads 8 -outfmt 6 -query "query.fa" -db "subject.db" -out out.out

Unfortunately, I'm really new to this and am not very knowledgable on the subject, but does it look like this command will give me the results I am looking for? Thanks for the help!
sam12 is offline   Reply With Quote
Reply

Tags
blast, blast+, blastn

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 03:51 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO