Conservation score calculation for gene sequences

Please suggest me some tools to calculate Conservation scores. Can we do it bu using Bioedit?

snp gene sequence

• 3,518 views • link

updated 9.6 years ago by Alex Reynolds

• written 11.3 years ago by muvinika •

2 answers

Not sure about your workflow. But one good score is CADD

http://cadd.gs.washington.edu/

Thank you

• 0 views • link

written 9.6 years ago by hns

PHAST offers phastCons and phyloP methods.

• 0 views • link

written 9.6 years ago by Alex Reynolds

More posts like this

How does Belvu calculate conservation scores?
written 5.1 years ago by jmungar2 •

I am using Belvu to calculate per-residue conservation scores but I could not find either in the manual nor in the SeqTools paper how conservation …
How to calculate the conservation score of a gene
written 6.0 years ago by yunzhe.jiang97 •

Hi! I am a freshman at comparative genomics. Now, I've got several sequences of genes, and I want to calculate the conservation scores of these …
How to determine consensus sequence and conservation score for each protein?
written 8.3 years ago by Kian •

How i can determine to consensus sequence and conservation score " percent of conservation" for some protein? i have some genes and i want to …
Pairwise alignment substitution matrix
written 11.1 years ago by muvinika •

As I need to align 2 gene sequences. Do I need to calculate PAM and BLOSUM scores. What is the difference between amino acid substitution …
Finding exon positions from cDNA sequence
written 11.3 years ago by muvinika •

Hi all, List some tools to find the position of exons in the cDNA sequence. Also help me if any package available in R.
Amino acid Changes Substitution score
written 11.3 years ago by muvinika •

Hi, How do we calculate Amino acid Changes Substitution score for mutations in the gene sequences? Could you please explain about the calculation of grantham …
How to calculate phastcons scores for overlapping transcripts with different strands
written 12.3 years ago by biorepine

Dear Biostars, I am trying to calculate conservation scores for overlapping sense and anti-sense pairs of transcripts. Previously I used phastcons scores from ENCODE(mm9) to …
How To Quantify The Significance Of The Conservation Of Dna Fragments
written 13.0 years ago by alteralex •

I have a genome, and each position has a conservation score. I want to identify the conserved fragments from these scores. A naive way would …
Is Any Database Provide Human Genes' Conservation Scores ?
written 13.4 years ago by Yu

Hi all Recently, I deal with some human gene data and I want to know if the gene I handled is conserved gene. Is any …
Calculating Conservation Score From Mutiple Sequence Alignment
written 14.7 years ago by Hari •

I would like to calculate conservation score of amino acids from a multiple sequence alignment,I would like to get a simple 2 column table with …