Finding Frequent To Rare Codon From The Codon Table Of Human

Question

[Elena]

how can i find frequent to rare codon from a nucleotide sequence? The frequent codons are those which are having the highest value for a particular amino acid in the codon table and the rare codons are those which are having the lowest value for the same amino acid.

For eg:

In Codon usage table of human: for the amino acid F, TTC -> TTT is the change from frequent to rare codon in the sequence

                   TTC=(0.54) and TTT= (0.46)

so, TTC is the frequent codon and TTT is the rare codon.

Can anyone tel me the concept behind finding solution to this problem. I ve been trying for long but couldn't get the solution for this problem.

Answer 1

[Michael Kuhn]

I'm not sure if you want to calculate this yourself or rely on existing tools, but what you're looking for is the Codon Adaptation Index. CAIcal is a webserver with further links to documentation and a paper describing the concept. They have also pre-calculated the codon table with frequencies for human.

[Elena]

actually from a given sequence after finding the synonymous SNP, from the Synonymous SNP what are the changes which are from frequent to rare i need to find out.

Answer 2

[Casey Bergman]

If you are looking for preferred (common) <-> unpreferred (rare) synonymous SNPs in coding regions based on a multiple sequence alignment of alleles, try DNAsp. This program is windows-based and not amenable to high throughput analysis, but if you have a small scale dataset, it should do what you are looking for.

[Cynthia]

i m trying with DNAsp, but its asking for 2 set of sequences. but i need to find out frequent to rare codons from the Synonymous SNPs in the individual sequence.

[Casey Bergman]

You'll need to reformat your SNP data as a multiple alignment, e.g. take your reference sequences and for each SNP sample, create a new sequence that replaces the reference nucleotide with the SNP variant (this will be sequence set 1). Then you'll need to align an outgroup sequence (this will be sequence set 2) to be able to polarize the changes, since without an outgroup you can't tell the direction of the mutation.

[Cynthia]

i m sorry but aligning an outgroup is bit confusing for me.

[Cynthia]

sorry sir ... aligning outgroup sequence in the sense? is it aligning distanly related species?

[Casey Bergman]

An outgroup does not need to be distantly related. It only needs to be outside the population under investigation, and can be from the same species. If you said what data you are working on, it would be easier to provide more specific advice.

[Cynthia]

i m workin on multiple sequence alignment of various organisms( like chimpanzee,rat, cat and many other mammals) for a breast cancer gene BRAD1. and i found the synonymous SNPs keeping human sequence as a template with other organisms. Now i need to identify the synonymous changes which are from frequent to rare for the nucleotide sequences of each individual species in a multiple sequence aligned file.

[Cynthia]

ok thanks for the idea... i ve got it

Answer 3

[Gareth Palidwor]

Keep in mind that codon usage bias in mammalian genomes is dominated by regional isochoric GC bias. This effect is strongest in human. The codon usage table gives you an average of codon usage across all coding sequences of the genome, but for any given gene the codon usage depends strongly on the local GC bias.

[Jason2]

Sorry I'm late to the party, but do you know of a paper that describes this phenomena?

Answer 4

[Larry_Parnell]

Try these links:

1. KEGG's codon usage table for human (which can be hard to find without this link). This was compiled from RefSeq genes
2. CodonExplorer

I don't find the difference between TTC at 0.54 and TTT at 0.46 so great as to warrant the labels of "frequent" and "rare."