Find gene models including alternative splicing events from genomic alignment of mRNA, EST and protein sequences.
Highlights:
User-supplied sequences are aligned against the genome map using the BLAT and SIM4 programs. Resulting exon connectivity is analyzed by applying graph-theoretic methods to build all possible gene models including splice variants.
The algorithm essentially combines the genome-based sequence clustering and transcript assembly procedures in a coherent fashion.
In addition to the user-supplied sequences, UniGene clusters and many well-known gene predictions such as Genscan, Ensembl and Acembly may be included in gene modeling.
The current implementation supports human, mouse and rat genomes.
