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PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text

By Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova and Paola Bonizzoni
Topics: Research
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:3358663
Provided by: PubMed Central
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    1. (2008). A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.
    2. (1997). Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology Cambridge:
    3. (2005). Birney E: Automated generation of heuristics for biological sequence comparison.
    4. (2002). BLAT-the BLAST-like alignment tool.
    5. (2006). Crollius HR: Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA. Genome Biology
    6. (2009). Detecting alternative gene structures from spliced ESTs: a computational approach.
    7. (2001). Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Research
    8. (2004). Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics
    9. (1996). Guigo R: Evaluation of Gene Structure Prediction Programs. Genomics
    10. (2002). Kornblihtt A: Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet
    11. (2004). M: ESTGenes: alternative splicing from ESTs in Ensembl. Genome Research
    12. (2010). MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Research
    13. (2006). MG: EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology
    14. Minimum factorization agreement of spliced ESTs.
    15. (2005). Pesole G: ASPIC: a novel method to predict the exonintron structure of a gene that is optimally compatible to a set of transcript sequences.
    16. (2006). Pesole G: ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.
    17. (2006). Pesole G: Computational methods for alternative splicing prediction.
    18. Pevzner PA: Splicing graphs and EST assembly problem. Bioinformatics 2002, 18(Suppl 1):S181-S188.
    19. (2008). Rätsch G: Optimal spliced alignments of short sequence reads. Bioinformatics
    20. (2005). S: ECgene: genome-based EST clustering and gene modeling for alternative splicing. Genome Research
    21. (2006). Sachidanandam R: Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Research
    22. (2009). SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics
    23. (2000). Solovyev V: Analysis of canonical and non-canonical splice sites in mammalian genomes.
    24. (2010). TC: Supersplat–spliced RNA-seq alignment. Bioinformatics
    25. (2004). The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome.
    26. (2004). The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Research
    27. (2005). Watanabe CK: GMAP: a genomic mapping and alignment program for mRNA and EST sequence. Bioinformatics

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