Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
cutadapt: A tool that removes adapter sequences mmartin Bioinformatics 132 05-19-2016 07:09 AM
small part of all 1000 sequences from 1000genomes data needed? culmen Bioinformatics 11 11-07-2012 10:23 AM
pre-filtering before running alignment: help needed angerusso Bioinformatics 2 11-15-2011 06:49 PM
Help needed to generate Consensus from alignment sarbashis Illumina/Solexa 0 08-10-2011 09:58 PM
The Best Tool for RNA Alignment EthoStrain Bioinformatics 5 09-07-2010 06:56 AM

Thread Tools
Old 11-09-2010, 03:18 PM   #1
Location: Heidelberg, Germany

Join Date: Aug 2010
Posts: 39
Default Needed: GAPed alignment tool to save my sequences from the SMART kit

Hi folks,

I'm looking for some recommendations. I've inherited some 454 sequences of cDNA generated using a SMART kit. Perhaps not surprisingly (sigh...see the sequences are contaminated with SMART kit adapters and giant swaths of As or Ts.

BUT, there is hope. Embedded within these sequences are the actual sequences of transcripts that I would like to align to a reference genome (of a closely related species). In effect, the sequences look like this:


Can anyone recommend an alignment tool that deals well with gaps such that the good sequence within the bad will align to the reference genome and the BAD portion will be dropped? Out of familiarity, I'm leaning towards using Blastz (or lastz), but there're a whole lot more alignment tools out there than the last time I did this.

Many thanks!

dagarfield is offline   Reply With Quote
Old 11-16-2010, 01:20 AM   #2
Senior Member
Location: WashU

Join Date: Aug 2010
Posts: 117

It seems like the next-gen, fast, short read aligners are generally focused on aligning entire reads and do not do substring alignments. You may be stuck using an old school aligner. BLAST will certainly do what you are describing. BLAT or Exonerate would also probably be fine. If you are aligning cDNAs to a genome you could also use splice aware aligners such as Spidey or Splign. Of course all of these options are way, way slower. Maybe someone else will suggest other options.
malachig is offline   Reply With Quote
Old 11-16-2010, 05:05 AM   #3
Senior Member
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323

As far as I can tell the 454 analysis tool will take care of the adapter for you. Have you tried it?
drio is offline   Reply With Quote
Old 12-10-2010, 05:58 AM   #4
Location: Heidelberg, Germany

Join Date: Aug 2010
Posts: 39
Default 454 adaptor removal

Thanks for the suggestion. In the end, the remove adaptor and repeat screen options on the 454 software did the trick just fine.
dagarfield is offline   Reply With Quote

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 03:01 AM.

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