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VVK in length

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This algorithm is for calculation of nucleotide content distribution between codon positions along the length of a coding district.

 

Instructions

You should enter your nucleotide sequence in the special cell on the "full sequence" list.

Than you should write the length of a separate peace of sequence (in codons) on "length" list.

Nucleotide content distribution between codon positions for each separate peace in which your sequence has just been cut will appear in the "content" list (in columns).

 

Interpretation of the results

Mutational pressure acting on the whole coding district should result in equivalent levels of nucleotide usage in third codon positions for all parts of this coding district. The violations from this rule may be due to existence of different kinds of mutational pressures acting on different parts of coding district, and more commonly due to frameshifting events, deletions and insertions happened not very long time ago.

 

Please, cite

Khrustalev V.V. HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it // In Silico Biology. 2009. Vol.9. Number 4. P.255-269. (Electronic version: Vol.9. 0022).

 

 

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