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ExORF:

Background:
The fundamental structure of the eukaryotic gene that distinguishes it from that of the prokaryotic gene is that its coding sequence is split into usually short coding pieces (exons) and usually long non-coding pieces (introns), whereas the prokaryotic gene's coding sequence is contiguous. According to the Random-sequence Origin of Split Genes (ROSG) concept, the coding sequence of a gene is split this way because the genes originated with this split structure intrinsically within prebiotically available random genetic sequences, wherein the random distribution of the stop-codons forced the coding sequence to be inherently short. Therefore the inherently long coding sequence of the gene could only be available in a split fashion with short exons. A powerful tool to correlate and analyze the exons to the ORF (sequence between successively occurring stop-codons) patterns of the split genes will greatly aid gene researchers. Exon-ORF Plotting (ExORF) tool enables the analysis of split-genes, correlating the exons of the gene with all the ORFs in the gene. It enables the ExORF analysis of genes, with many interactive graphical and statistical capabilities.

ExORF database and software tools are a great boon to researchers and students for understanding the origin of the split structure of the genes, and several aspects of the statistics of these features within genes. They also aid in correlating these structures across the genomes of different organisms, thereby leading to the understanding of the evolutionary relationships among these genes, and thereby these organisms.

Description:
ExORF database provides the Exon-ORF plots of the gene and its spliced sequence, ARF (Amino acid codon frame) plots, spliced ARF plots, ORF length distribution plots, and the plots of stop-codons in splice signal sequences of genes. The user can switch on or off the exon plot or the ORF plot or the vice versa. One can visualize the distribution of the ORF lengths of the split gene and the spliced gene sequence, displaying the statistical distributions of the ORFs in both. The plot from every gene illustrates the ROSG concept of the generation of one long ORF from the short ORFs of the split gene that contains the spliced coding sequence of the gene.

Features:

The ExORF web interface provides the face page for the ExORF analysis of eukaryotic genomes and prokaryotic genomes.
All of the genes of each genome can be analyzed using the ExORF software tool.
For each gene, the plot provides the list of exon lengths and positions, the ORF plots in three reading-frames (RFs) with the different exons embedded and overlaid in the appropriate RF in which the exon lies.
Each plot also provides the ORF plot of the spliced gene sequence, and the overlaid plot of the spliced coding sequence (all the exons of the gene spliced together thereby eliminating all the intron sequences).
Each ExORF provides two control studies: 1) the ARF plot, which plots the distances between any three of the non-stop codons (61/64 codons) of the split-gene, and the ARF plot of the spliced gene sequence, showing that the patterns are qualitatively the same, without leading to any statistically long ARF in the spliced gene sequence. 2) ExORF of a computer generated random DNA sequence, showing that the patterns of the ORFs are extremely similar to that of the split-genes of intron-rich genomes such as that of the human.
The ExORF for each gene also provides the ability to visualize the statistical graph of the distribution of the ORF lengths of the split gene sequence and the spliced gene sequence, wherein one very long, statistically outlying, ORF is generated within the spliced gene sequence.
The ExORF of each gene demonstrates that the splice signal sequences on both ends of the exons (or introns) contain one of the three stop codons (TAG, TAA or TGA) at precisely the border of the exons and introns.

Applications:

For the first time, ExORF enables the analysis of the split-genes correlating with the stop-codons and the ORFs of the genes.
Researchers can analyze the origin of the split structure of the gene using ExORF.
ExORF also shows the unique patterns of the stop-codon and ORF distribution as correlated with those of exons, which is not possible by any other tool.
The available long ORFs which may contain potential exons that are currently empty in genes can be analyzed for potential new genes surrounding them.
There are differences in the length of the exons in the genomes of the different organisms, especially correlating with the size of the genome and the complexity of the organism. Thus, ExORF is an excellent tool to analyze the evolutionary relationships between the different organisms correlated to the ExORF patterns.
Besides being a powerful research tool, ExORF is an excellent teaching resource with a plethora of genes from many genomes, and with the software capability to carry out a variety of research and analysis in an easy user-friendly manner.
Human ExORF Plots ( http://66.170.16.154/chandancn/human ), ( Username : genome ; password : sgopgic )