ArticleNucleic acids research2004
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity.Current genomics · 2013Article
- Steroid receptor RNA activator protein binds to and counteracts SRA RNA-mediated activation of MyoD and muscle differentiation.Nucleic acids research · 2011Article
- EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data.BMC bioinformatics · 2009Article
- Genomic landscape of developing male germ cells.Birth defects research. Part C, Embryo today : reviews · 2009Review
- Iterative gene prediction and pseudogene removal improves genome annotation.Genome research · 2006Article
- Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.Nucleic acids research · 2006Article
- ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs.Nucleic acids research · 2005Article
- ECgene: genome-based EST clustering and gene modeling for alternative splicing.Genome research · 2005Article
- ECgene: genome annotation for alternative splicing.Nucleic acids research · 2005Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing is in important mechanism of modulating gene function and expression which greatly expands transcriptome diversity. ASmodeler is a novel web-based utility that finds gene models including alternative splicing events from genomic alignment of mRNA, EST and protein sequences. 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. ASmodeler is available at http://genome.ewha.ac.kr/ECgene/ASmodeler/.
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Registered trials
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