This application translates protein sequences into DNA sequences using predefined codon usage tables in combination with a set of predefined rules provided by users on site. The aim of this application is to rewrite genes to be better expressed in a different species.
1) This app will allow users to enter multiple protein sequences (represented as strings of 20 letters) in Fasta format (a simple text format), select a codon table, define a codon usage cut off rate and restriction sites to be eliminated and convert it to DNA sequences (in the form of strings of 4 letters).
2) During the converting process the program will also check for the presence of a bunch of DNA sequences and eliminate them if they present. It is expected that not all of the requirements might be fulfilled for a particular DNA sequence, in which case the minor requirements can be ignored.
3) The process will run a number of rounds (e.g. 100 t0 1000 times) depending on the hardware requirements software efficiency to generate the most desirable sequences.
4) Optional: candidate sequences will be fed into an external program for evaluation and ranking.
5) The generated sequences will be presented in simple Fasts format with and without corresponding protein sequence. In addition a graph of the GC content of the sequence should also be presented.
6) We have someone already initiate the work, and it is in the attachment, but it does not meet our full requirements. We need someone to continue this work.
7) A web developer with strong bioinformatics background is strong preferred.