Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
BLAT of sequence to dog/human reference confounding tracecakes Bioinformatics 0 11-10-2013 04:00 PM
BLAT or BLAST: output SNPs between reference and query? bbimber Bioinformatics 1 02-23-2010 11:59 AM
BLAT settings for 17bp sequences? DrD2009 Bioinformatics 3 11-18-2009 07:41 AM
maq map/match settings in colorspace der_eiskern Bioinformatics 0 07-28-2009 02:10 PM
Perfect match disagreement between bowtie and BLAT on human genome danielsbrewer Bioinformatics 3 03-10-2009 10:10 PM

Thread Tools
Old 08-26-2014, 05:04 PM   #1
Alex Lee
Junior Member
Location: N. Cal

Join Date: Apr 2014
Posts: 10
Default BLAT settings to match is continuously on reference?

HI I have 100 bp sequences I would like to match against a reference region. Is there a way I can set BLAT so that the match (eg 80%) is continuous? For example what I don't want is for the the first 50 bp to match then follow by X amount of bp from the reference region then match again for the last 50 bp. In other words I would like to the ability to set X, for example no more than 2 bp.

in short I would like to be able to set how many N's are betwen the two matches: match NNNNNN match

hope this is clear and someone can help. Thanks!
Alex Lee is offline   Reply With Quote

blast, blat, match position, query coverage

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 04:11 PM.

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