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Category:Resource:Alternative Splicing Annotation Project II Database
Abbrev ASAP II  +
Availability THIS RESOURCE IS NO LONGER IN SERVICE +, Documented on 8/12/13. +
CurationStatus curated  +
DefiningCitation http://www.bioinformatics.ucla.edu/ASAP2  +
Definition THIS RESOURCE IS NO LONGER IN SERVICE, doc THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. An expanded version of the Alternative Splicing Annotation Project (ASAP) database with a new interface and integration of comparative features using UCSC BLASTZ multiple alignments. It supports 9 vertebrate species, 4 insects, and nematodes, and provides with extensive alternative splicing analysis and their splicing variants. As for human alternative splicing data, newly added EST libraries were classified and included into previous tissue and cancer classification, and lists of tissue and cancer (normal) specific alternatively spliced genes are re-calculated and updated.<br /> They have created a novel orthologous exon and intron databases and their splice variants based on multiple alignment among several species. These orthologous exon and intron database can give more comprehensive homologous gene information than protein similarity based method. Furthermore, splice junction and exon identity among species can be valuable resources to elucidate species-specific genes. ASAP II database can be easily integrated with pygr (unpublished, the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc. ASAP II can be searched by several different criteria such as gene symbol, gene name and ID (UniGene, GenBank etc.). The web interface provides 7 different kinds of views: (I) user query, UniGene annotation, orthologous genes and genome browsers; (II) genome alignment; (III) exons and orthologous exons; (IV) introns and orthologous introns; (V) alternative splicing; (IV) isoform and protein sequences; (VII) tissue and cancer vs. normal specificity. ASAP II shows genome alignments of isoforms, exons, and introns in UCSC-like genome browser. All alternative splicing relationships with supporting evidence information, types of alternative splicing patterns, and inclusion rate for skipped exons are listed in separate tables. Users can also search human data for tissue- and cancer-specific splice forms at the bottom of the gene summary page. The p-values for tissue-specificity as log-odds (LOD) scores, and highlight the results for LOD >= 3 and at least 3 EST sequences are all also reported.<br /> quences are all also reported.<br />
Grant Category:U54 RR021813   +, Category:DE-FC02-02ER63421   +
Has default formThis property is a special property in this wiki. Resource  +
Has role Database +
Id nif-0000-02572  +
Is part of University of California at Los Angeles; California; USA +
Keywords Exon +, Gene structure +, Genome +, Alternative splicing +, Cancer genome alignment +, Intron +, Isoform +, Orthologous exon +, Orthologous gene +, Orthologous intron +, Protein sequence +, Splice site +, Tissue +, Genome alignment +, Cancer +
Label Resource:Alternative Splicing Annotation Project II Database  +
Modification dateThis property is a special property in this wiki. 7 October 2014 18:36:22  +
ModifiedDate 7 October 2014  +
PMID 17108355  +
Page has default formThis property is a special property in this wiki. Resource  +
Species Vertebrata +, Human +, Insecta +, Nematoda +
SuperCategory Resource  +
Supporting Agency National Institutes of Health +, United States Department of Energy +, Dreyfus Foundation Teacher-Scholar Award +
Synonym Alternative Splicing Annotation Project II  +, ASAP II Database  +
Categories Resource
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Resource:ASAP: the Alternative Splicing Annotation Project + RelatedTo
 

 

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