RBS FINDER (Ribosomal Binding Sites) : RBS FINDER (Ribosomal Binding Sites)
Slide 2 : RBS (Ribosomal Binding sites)
At the initiation of protein synthesis, the ribosomal binds to a region near the 5’end of the mRNA known as RBS.
The RBS is the region where the ribosome binds to an mRNA to begin the translation of the mRNA in to a protein.
The RBS are the signals that can help in the identification of a gene.
Slide 3 : RBS sequence are rich in purine bases (Adenine and Guanine).
The RBS is typically located about 8-10 base pairs prior to the translation start site
The RBS finding assumes that at least some of the start codons have been predicted correctly by the gene identification system.
Slide 4 : The RBS is one of those important signals for the identification of the genes in a DNA sequence, since almost every bacterial mRNA has an RBS, to the polypeptidical product to be produced.
Slide 5 : RBS FINDER (Ribosomal Binding Sites)
RBS Finder is the prediction of Ribosomal Binding Sites.
RBS Finder is normally run as a post processor to the Glimmer gene finder or to other prokaryotic gene finders.
Slide 6 : RBS Finder will search for regions in the vicinity of the gene start whole the ribosome might bind.
Based on its finding RBS Finder might propose a different gene start.
The use of the RBS Finder increase the accuracy of prediction of the gene start.
Slide 7 : GLIMMER
Glimmer is a gene detector.
The input to glimmer is a single DNA sequence fasta format.
Glimmer uses an interpolated markov model to detect the locations of genes.
Glimmer will use IIM to analyze the input sequence.
Slide 8 : When RBS Finder proposes a different start the finding of Glimmer as well as alternative gene start from RBS Finder are taken into the results.
Trans Term is a program that finds rho-independent transcription terminators in bacterial genomes and evaluates the accuracy of its prediction.
Each terminator found by the program assigned a confidence value, provides an estimate of its probability of being true terminator.