Mapping the dN/dS values
Hi!
Which program do you recommend for mapping the dN/dS values per residue in the protein crystal structure?
Thank!
sequence
dn/ds
• 1,236 views
•
link
written
by
mauricio.1313
0
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
PAML Troubleshooting Help
written by sebabiokr 1Hi Im using the paml program for the (dN) and (dS) substitution ratio (dN/dS) of genes. i run the CODEML/codeml4.10.6 codeml-sites.ctl | tee logfile_codeml-sites.txt but …
-
How find the best model for calculate dN/dS with big data (727 sequences)?
written by mauricio.1313 0Hi! I´m working on my thesis project to calculate dN/dS with CODEML, my data have 727 sequences. I have 3 different proteins (727 sequences each …
-
Suggestions for analyze dN, dS rate and omega (dN/dS ratio) result?
written by mauricio.1313 0Hi! I´m working on my project thesis with 3 different viral proteins from 23 different viruses. I made a pairwise comparison with Yiang and Nielsen …
-
Substitution model for a viral genome in RAxML
written by mauricio.1313 0Hi! Which substitution model do you recommend for viral genomes (nucleotides) in RAxML? I will do the following analysis "Rapid Boostrap + ML" I think …
-
Hypothetical protein in Prokka
written by mauricio.1313 0Hi! What to do with the hypothetical protein in Prokka? Some program to improve this metric? Thank you!
-
Help with understanding PAML M0 output
written by DNAngel 26Hi all, Could someone just clarify the following output for me? Example output: branch t N S dN/dS dN dS N*dN S*dS 38..1 0.431 2257.5 …
-
Calculate dN/dS ratio for protein coding genes using PAML
written by b.shrestha 1Hi, I am trying to calculate dN/dS ratio for protein coding genes. I have sequence alignment for a protein coding gene for about 30 species …
-
Residue Conservation: Sequence Logo Vs Codeml Or Rate4Site
written by Pappu 210<p>I made a sequence logo from an alignment of homologous protein sequences. I can clearly see the residue conservation in it. However I read a …
-
What'S The Biological Meaning Between Two Group (They All Same Family) When Dn/Ds Less Than 1 But O…
written by harrymao20 0<p>for detail one protein X by dNdS calculation</p> <p>fish urchin dN/dS =0.5</p> <p>human mus dN/dS = 0.01</p> <p>what’s the biological meaning between two group</p> <p>how …
-
Dn/Ds Ratio - Paml : How Is It Possible To Obtain Negative Values For Dn Or Ds ?
written by Francois Olivier Hébert 28<p>Hi,</p> <p>I have a set of 383 coding sequences in which there is a whole bunch of SNPs. I only have two species (2 populations …
What are some programs you've looked at/compared?