Name
Title | ||
|---|---|---|
The Asap Ii Database: Analysis And Comparative Genomics Of Alternative Splicing In 15 Animal Species |
Abstract | ||
|---|---|---|
We have greatly expanded the Alternative Splicing Annotation Project (ASAP) database: (i) its human alternative splicing data are expanded similar to 3-fold over the previous ASAP database, to nearly 90 000 distinct alternative splicing events; (ii) it now provides genome-wide alternative splicing analyses for 15 vertebrate, insect and other animal species; (iii) it provides comprehensive comparative genomics information for comparing alternative splicing and splice site conservation across 17 aligned genomes, based on UCSC multigenome alignments; (iv) it provides an similar to 2- to 3-fold expansion in detection of tissue-specific alternative splicing events, and of cancer versus normal specific alternative splicing events. We have also constructed a novel database linking orthologous exons and orthologous introns between genomes, based on multigenome alignment of 17 animal species. It can be a valuable resource for studies of gene structure evolution. ASAP II provides a new web interface enabling more detailed exploration of the data, and integrating comparative genomics information with alternative splicing data. We provide a set of tools for advanced data-mining of ASAP II with Pygr (the Python Graph Database Framework for Bioinformatics) including powerful features such as graph query, multigenome alignment query, etc. ASAP II is available at http://www.bioinformatics.ucla.edu/ASAP2. |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1093/nar/gkl884 | NUCLEIC ACIDS RESEARCH |
Keywords | Field | DocType |
data mining,introns,alternative splicing,comparative genomics,exons,gene structure,internet,sequence alignment,web interface,genomics | Sequence alignment,Graph database,Biology,Exon,Alternative splicing,Genomics,Comparative genomics,RNA splicing,Intron,Genetics,Molecular biology | Journal |
Volume | Issue | ISSN |
35 | Database issue | 0305-1048 |
Citations | PageRank | References |
19 | 1.19 | 11 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Namshin Kim | 1 | 109 | 8.72 |
| Alexander V. Alekseyenko | 2 | 37 | 9.10 |
| Meenakshi Roy | 3 | 19 | 1.19 |
| Christopher Lee | 4 | 375 | 40.57 |