HyPhy message board

	Welcome, Guest. Please Login

Home

Help

HyPhy message board › Methodology Questions › How to › SCUEAL

(Moderators: Sergei, Simon)

‹ Previous Topic | Next Topic ›

Pages: 1

Send Topic

SCUEAL (Read 2432 times)

CrystalH

YaBB Newbies

Offline

Feed your monkey!

Posts: 23

SCUEAL
Jun 1^st, 2011 at 1:31pm

Hello,
I have successfully created HIV envelope and gag reference datasets using the Los Alamos subtype reference alignments in the correct format for SCUEAL. From a previous posting, I understand that leaving gapped regions in the query sequences is okay, but is it better to remove gapped regions (although the gapped regions are present in the reference dataset)? Is SCUEAL likely to misidentify heterotachy as breakpoints or is it similar to GARD, where KH testing is used to designate whether a breakpoint is strongly supported? Thank you! Cool

-Crystal Hepp

Also, I can pass along the reference datasets to you that I made for the gag and env if you are interested.

IP Logged

Sergei

YaBB Administrator

Offline

Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male

Re: SCUEAL
Reply #1 - Jun 1^st, 2011 at 2:17pm

Hi Crystal,

Leaving gapped regions is indeed OK, but there could be some issues if there are very long gapped regions (e.g. over 100 bp in a given sequences). SCUEAL explicitly tests for topological incongruence, so heterotachy is not a problem. If the LANL references data sets contains CRFs, it needs to be processed differently, i.e. do NOT run MakeReferenceAlignment.bf on them as this will assume that a single tree is adequate to explain all regions of the alignment (which is not the case with CRFs). If you used BuildupReferenceAlignment.bf, that will be taken care of. Finally, some of the reference sequences in LANL seemed to be intra-subtype recombinants, which could also be a problem if you used MakeReferenceAlignment.bf

Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

WWW

IP Logged

CrystalH YaBB Newbies Offline Feed your monkey! Posts: 23	Re: SCUEAL Reply #2 - Jun 1^st, 2011 at 2:34pm Thank you! The gapped areas are typically 10-50 nt (usually at the variable regions in env). Actually I recently read the SCUEAL paper and I plan on mimicking your reference dataset generation method to make sure I have acceptable datasets...and I am not interested in CRFs, so those are left out. Thanks again!
Back to top	IP Logged

Pages: 1

Send Topic

‹ Previous Topic | Next Topic ›

« Home

‹ Board

Top of this page