Methods of parallel gene cloning and analysis

This invention provides the systematic and oriented codon-based high-throughput methods for the identification of both known and unknown sequences. The identification are focused on the sequences of ORF of the gene and the corresponding transcriptional and translational products (RNA and peptide sequences) such as 5'-end from the start codon, 3'-end from the stop codon and two consecutive codon sequence which is recognized by a restriction enzyme between 5'-end and 3'-end of a sequence. The present invention provides the relevant genetic algorithms for the sequence identification and library construction, such as 61.sup.(n-1)/(0.sup.(n-1), 61.sup.n/20.sup.n, 61.sup.(n-2)/20.sup.(n-2). It also provides the genetic algorithms of 64.sup.(n-1) and 64.sup.n to define 5'-UTR, 3'-UTR in order to deduce oligonucleotide sequences which span start codon and stop codon respectively. The present invention classified oligonucleotides in accordance with the G+C content to provide uniformed hybridization conditions. Applications include PCR, cloning, dot-blot hybridization, library construction, sequence determination, signature sequence and signature signal identification, ELISA, DNA and protein microarrays.