How to improve sequence alignment?!
Hi everyone,
I am noticing that Modeller does not do a good job when it comes to sequence alignment of short peptides or DNA sequences. For example, please see the the comparison below:
(1) Modeller alignment: Template GTPPPP - - YTVG Peptide TVLPPPPYRHRN
(1) ClustalW alignment: Template -GTPPPPYTVG- Peptide TVLPPPPYRHRN
As you can see, Modeller is unable to align up properly the central PPPPY motif in my peptide with the template!! In contrast, ClustalW is spot on in its ability to recognize a key pattern in the sequence.
Is there a way to improve sequence alignment in Modeller? How can I make changes to the following Modeler file that I am using for my sequence alignment:
# Make a pairwise alignment of two sequences aln = alignment(env, file='template.ali') aln.salign(overhang=30, gap_penalties_1d=(-450, -50), alignment_type='tree', output='ALIGNMENT') aln.write(file='template.pir', alignment_format='PIR') aln.write(file='template.pap', alignment_format='PAP')
What parameters or settings, if any, could be changed in the above setup to improve sequence alignment in Modeller?
Thank you so much for your advice and any comments that you may have.
*AMJAD FAROOQ PhD DIC | Associate ProfessorDept of Biochemistry & Molecular Biology | Miller School of Medicine | University of Miami | Miami | FL 33136Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 33136 amjad@farooqlab.net amjad@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net http://www.farooqlab.net*
On 11/13/13 8:28 AM, Amjad Farooq wrote: > I am noticing that Modeller does not do a good job when it comes to > sequence alignment of short peptides or DNA sequences.
You're not required to use Modeller to make modeling alignments - as long as you can make alignment files in the PIR format Modeller wants, you can use any package (including ClustalW).
That said, by default Modeller's alignment methods use global alignment and so try to align the termini, since this is typically what you want for modeling. You can adjust the overhang parameter to discourage this behavior, or use local alignment.
Ben Webb, Modeller Caretaker
Thanks Ben!
I modified the script accordingly:
# Make a pairwise alignment of two sequences aln = alignment(env, file='template.ali') aln.salign(overhang=5, gap_penalties_1d=(-450, -50), alignment_type='pairwise', output='ALIGNMENT') aln.write(file='template.pir', alignment_format='PIR') aln.write(file='template.pap', alignment_format='PAP')
It worked beautiful.
On Wed, Nov 13, 2013 at 4:34 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 11/13/13 8:28 AM, Amjad Farooq wrote: > >> I am noticing that Modeller does not do a good job when it comes to >> sequence alignment of short peptides or DNA sequences. >> > > You're not required to use Modeller to make modeling alignments - as long > as you can make alignment files in the PIR format Modeller wants, you can > use any package (including ClustalW). > > That said, by default Modeller's alignment methods use global alignment > and so try to align the termini, since this is typically what you want for > modeling. You can adjust the overhang parameter to discourage this > behavior, or use local alignment. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
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Modeller Caretaker