|
|
From NeuroLex
| Abbrev
|
ASAP II +
|
| CurationStatus
|
curated +
|
| DefiningCitation
|
http://www.bioinformatics.ucla.edu/ASAP2 +
|
| Definition
|
<br />
ASAP II is an expanded versi … <br />
ASAP II is an expanded version of the 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 />
We 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 ASAP II database can be easily integrated with pygr (unpublished, the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc.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 +,
Insects +,
Intron +,
Isoform +,
Orthologous exon +,
Orthologous gene +,
Orthologous intron +,
Protein sequence +,
Splice site +,
Tissue +,
Vertebrate species +,
Nematodes +,
Human +,
Genome alignment +,
Cancer +
|
| Label
|
Resource:Alternative Splicing Annotation Project II Database +
|
| Modification dateThis property is a special property in this wiki.
|
29 July 2011 21:39:16 +
|
| ModifiedDate
|
29 July 2011 +
|
| PMID
|
17108355 +
|
| Page has default formThis property is a special property in this wiki.
|
Resource +
|
| 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
|
|
|
