SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Searching bases in reference genome. kasthuri Bioinformatics 2 01-12-2012 04:54 AM
gene searching in whole genome JohnLuther Bioinformatics 2 12-02-2011 09:36 AM
Searching for paired reads around a location Ash Bioinformatics 2 10-12-2011 03:21 AM
searching for contigs and paired data boetsie General 0 08-06-2010 02:11 AM

Reply
 
Thread Tools
Old 07-14-2011, 01:46 AM   #1
seq_GA
Senior Member
 
Location: Asiana

Join Date: Feb 2009
Posts: 124
Default Adapter searching

Hi,
We are having Illumina paired end sequenced data with adapters in both 3' and 5' tags.

Is there any open source software to fish for adapters in both 3' (7 bps long) and 5'(6 bps long). Rght now we are using smith-waterman to do local alignment allowing 2 mismatches. Tags are from Illumina sequencing and hence 3' or 5' adapter cab be found in eirther read1 or read2 of Illumina paired end sequnced data.

The whole process is very slow because of smith-waterman.

I am looking for a tool which can look for both 3' and 5' adapter allowing 2 mismatches in the adapter.

Thanks.
seq_GA is offline   Reply With Quote
Old 07-14-2011, 03:29 AM   #2
gaffa
Member
 
Location: Gothenburg/Uppsala, Sweden

Join Date: Oct 2010
Posts: 82
Default

Here are some alternatives, some of these can probably do the job: http://biostar.stackexchange.com/que...ation-illumina
gaffa is offline   Reply With Quote
Old 07-14-2011, 08:33 AM   #3
BAMseek
Senior Member
 
Location: St. Louis, MO, USA

Join Date: Apr 2011
Posts: 124
Default

Hi seq_GA,

Some of the trimming algorithms use Hamming distance (only looking at mismatches and not indels). These would probably be faster than a Smith-Waterman since the search space is smaller.

For methods that accommodate indels, you might try Btrim: it uses an optimized Smith-Waterman implementation using bit-level parallelism. I haven't tried the program myself (only available on Linux and no source code), but I think it is an interesting approach.

Justin
BAMseek is offline   Reply With Quote
Old 07-18-2011, 01:48 AM   #4
NicoBxl
not just another member
 
Location: Belgium

Join Date: Aug 2010
Posts: 263
Default

cutadapt is pretty good too : http://code.google.com/p/cutadapt/
NicoBxl 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 02:41 PM.


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