Six-frame translation

Identify the functionally active frame of translation by comparing the results of (a) six frame translations with Translate tool of ExPASy or ORF prediction with ORF Finder of NIH and (b) ORFGene of WebGene. 

There are three varieties of translated BLAST search tblastn, blastx, and tblastx. In the first variant, tblastn, a protein sequence query is compared to the six-frame translations of the sequences in a nucleotide database. In the second variant, blastx, a nucleotide sequence query is translated in six reading frames, and the resulting six-protein sequences are compared, in turn, to those in a protein sequence database. In the third variant, tblastx, both the query and database subject nucleotide sequences are translated in six reading frames, after which 36 (6 x 6) protein blastp comparisons are made. Protein sequences... 

Translate the DNA sequence into a protein sequence, searching all six frames... 

Without any doubt, mass spectrometry is now the most efficient way to identify proteins [75-78], The method is based on comparison of the data obtained from the mass spectrometry with those predicted for all the proteins contained in a database. The efficiency of the method results from the development of mass spectrometry into a rapid and sensitive method to analyse peptides and proteins and also from the availability of larger and larger databases. In October 2006, these databases contained more than 2400000 non-redundant sequences. Furthermore, the data obtained from genomic sequences after translation in the six lecture frames also can be used. The databases based on expressed sequence tags (ESTs) are another usable source for search. They are composed of sequences based on cDNA fast sequencing. They are limited to short lengths, about 300 bases, and contain many errors but they correspond to coding sequences. Despite their defects, they are very useful for identification of proteins by mass spectrometry [79]. 

Frames shows open reading frames for the six translation frames of a DNA sequence. 

The nucleotide sequence of the 1.8-kb EcoRl-Sall fragment from the genomic DNA revealed a single open reading frame (ORF) [25]. Translation of the ORF encoded the predicted protein of 388 amino acids with an Mr of 42,033 and an amino acid-sequence identical to those obtained by NH2-terminal amino acid sequencing of the six peptides prepared from purified ADP. Considering that ADP was secreted in the culture broth and that the Mr of the predicted ORF... 

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