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1.  AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts 
Bioinformatics  2012;28(15):2076-2077.
Summary: Alternative Splicing Effects ASsessment Tools (AS-EAST) is an online tool for the functional annotation of putative proteins encoded by transcripts generated by alternative splicing (AS). When provided with a transcript sequence, AS-EAST identifies regions altered by AS events in the putative protein sequence encoded by the transcript. Users can evaluate the predicted function of the putative protein by inspecting whether functional domains are included in the altered regions. Moreover, users can infer the loss of inter-molecular interactions in the protein network according to whether the AS events affect interaction residues observed in the 3D structure of the reference isoform. The information obtained from AS-EAST will help to design experimental analyses for the functional significance of novel splice isoforms.
Availability: The online tool is freely available at http://as-alps.nagahama-i-bio.ac.jp/ASEAST/.
Contact: m_shionyu@nagahama-i-bio.ac.jp
doi:10.1093/bioinformatics/bts320
PMCID: PMC3400965  PMID: 22645168
2.  RESOPS: A Database for Analyzing the Correspondence of RNA Editing Sites to Protein Three-Dimensional Structures 
Plant and Cell Physiology  2009;50(11):1865-1873.
Transcripts from mitochondrial and chloroplast DNA of land plants often undergo cytidine to uridine conversion-type RNA editing events. RESOPS is a newly built database that specializes in displaying RNA editing sites of land plant organelles on protein three-dimensional (3D) structures to help elucidate the mechanisms of RNA editing for gene expression regulation. RESOPS contains the following information: unedited and edited cDNA sequences with notes for the target nucleotides of RNA editing, conceptual translation from the edited cDNA sequence in pseudo-UniProt format, a list of proteins under the influence of RNA editing, multiple amino acid sequence alignments of edited proteins, the location of amino acid residues coded by codons under the influence of RNA editing in protein 3D structures and the statistics of biased distributions of the edited residues with respect to protein structures. Most of the data processing procedures are automated; hence, it is easy to keep abreast of updated genome and protein 3D structural data. In the RESOPS database, we clarified that the locations of residues switched by RNA editing are significantly biased to protein structural cores. The integration of different types of data in the database also help advance the understanding of RNA editing mechanisms. RESOPS is accessible at http://cib.cf.ocha.ac.jp/RNAEDITING/.
doi:10.1093/pcp/pcp132
PMCID: PMC2775959  PMID: 19808808
Chloroplast; Mitochondrion; Molecular evolution; Organelle genome; Protein 3D structure; RNA editing
3.  AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse 
Nucleic Acids Research  2008;37(Database issue):D305-D309.
We have constructed a database, AS-ALPS (alternative splicing-induced alteration of protein structure), which provides information that would be useful for analyzing the effects of alternative splicing (AS) on protein structure, interactions with other bio-molecules and protein interaction networks in human and mouse. Several AS events have been revealed to contribute to the diversification of protein structure, which results in diversification of interaction partners or affinities, which in turn contributes to regulation of bio-molecular networks. Most AS variants, however, are only known at the sequence level. It is important to determine the effects of AS on protein structure and interaction, and to provide candidates for experimental targets that are relevant to network regulation by AS. For this purpose, the three-dimensional (3D) structures of proteins are valuable sources of information; however, these have not been fully exploited in any other AS-related databases. AS-ALPS is the only AS-related database that describes the spatial relationships between protein regions altered by AS (‘AS regions’) and both the proteins’ hydrophobic cores and sites of inter-molecular interactions. This information makes it possible to infer whether protein structural stability and/or protein interaction are affected by each AS event. AS-ALPS can be freely accessed at http://as-alps.nagahama-i-bio.ac.jp and http://genomenetwork.nig.ac.jp/as-alps/.
doi:10.1093/nar/gkn869
PMCID: PMC2686549  PMID: 19015123
4.  Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs 
Nucleic Acids Research  2006;34(14):3917-3928.
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants.
doi:10.1093/nar/gkl507
PMCID: PMC1557807  PMID: 16914452

Results 1-4 (4)