ASmodeler -- Gene Modeling of Alternative Splicing from Genomic Alignment of mRNA, EST and Protein Sequences

What you can do:
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.
Keywords:
  • gene splicing
  • alternative splicing
  • splice variants
  • gene modeling
  • exons
  • introns
Literature & Tutorials:
PubMed Link: ASmodeler
This record last updated: 05-09-2005

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