How to compare the alignment quality of two or more homology modelling software

I am generating a high quality model by homology modeling method. But I am looking at alignment from different software , alignment between my target sequences from blast and other alignmet from HHpred. saw I want to compare the quality of the two alignment , any suggestion how can I do that ?

alignment

• 1,861 views • link

updated 9.8 years ago by GenoMax

• written 9.8 years ago by roonymoonlight •

t-coffee provides good alignment comparison methods for structural alignments here

• 0 views • link

written 9.8 years ago by microfuge

0 answers

No answers yet.

More posts like this

MUSCLE Protein Alignment of Distantly Related Proteins
written 2.7 years ago by Richard Fontaine •

Hello everyone, I am trying to infer phylogenetic relationships between a set of approximately 60 proteins. They are all putative antibacterial proteins, but their sequences …
How to identify different protein domains using HHpred
written 4.5 years ago by MicrobePrincess •

I am new to HHpred/ analyzing proteins so bare with me. I have been given an uncharacterized protein, whose FASTA sequence I have obtained from …
RSMD in homology modelling protein
written 8.8 years ago by l.souza

Hello everyone, I am modeling a protein through homology approach. My protein has a large disordered structure (~46% of coil). After the refinement, the RSMD …
Multiple sequence alignment to find conserved regions
written 9.5 years ago by fabbrl •

Hi all! I am doing homology modeling for a transmembrane protein (sodium channel). I am still in the phase of aligning the sequences (query and …
What is the differenc between the alignment generated by HHpred and the one generated by BLAST?nd h…
written 9.8 years ago by roonymoonlight •

Hi, I am trying to generate a high quality model for GPR146 by homology modelling method ( I will use modeller) .As you know a …
Protein modelling with modeller
written 10.1 years ago by Shamim Sarhadi

Hi I am a newbie in protein modeling, I create a model for my aa sequence with modeller and I-TASSER (zhang lab server), now I …
How to evalute homology models of Multi - domain protein based on multiple template?
written 11.5 years ago by joice624 •

Hi, I built a homology model of a protein with multiple domains and the templates I used each contain only fragments of the protein obtained …
Theoritical Modeling
written 14.1 years ago by nilav25 •

<p>dear all, I am a beginner of bioinformatics. i am doing homology modeling of 2 proteins. But i have done this using automated mode of …
Full Structure Of Protein Sequence
written 14.4 years ago by Sheila

<p>Hello, I have some protein sequences and looking for structures. Doing a blast search in PDB gives many hits but they do not cover full …
Homology Modeling With High Sequence Identity
written 14.4 years ago by Raghul

<p>Hi to all, When trying to build a homology modeling for a protein with high sequence identity (>80%)with PDB structure using SwissModel with "alignment mode" …