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EST2GENOME application details page
Align EST and genomic DNA sequences
est2genome is a software tool to aid the prediction of genes bysequence homology. The program will align a set of spliced nucleotidesequences (ESTs cDNAs or mRNAs) to an unspliced genomic DNA sequence,inserting introns of arbitrary length when needed. In addition, wherefeasible introns start and stop at the splice consensus dinucleotidesGT and AG. Unless instructed otherwise, the program makes three alignments: Firstit compares both stands of the spliced sequence against the forwardstrand of the genomic, assuming the splice consensus GT/AG (ie in theforward gene direction). The maximum-scoring orientation is thenrealigned assuming the splice consensus CT/AC (ie in the reversed genedirection). Only the overall maximum-scoring alignment is reported. The program outputs a list of the exons and introns it has found. Theformat is like that of MSPcrunch, ie a list of matching segments. Thisformat is easy to parse into other software. The program alsoindicates, based on the splice site information, the gene's predicteddirection of transcription. Optionally the full sequence alignment isprinted as well (see the example).
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