Difference between revisions of "About"
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| − | PastDB is a database of Alternative Splicing (AS) profiles across multiple tissues and environmental conditions of <i>Arabidopsis thaliana</i>. PastDB contains AS events (including exon skipping, alternative 5' and 3' splice sites and retained introns). AS event identification and sequence inclusion level quantification in RNA-seq samples have been performed with [https://github.com/vastgroup/vast-tools | + | PastDB is a database of Alternative Splicing (AS) profiles across multiple tissues and environmental conditions of <i>Arabidopsis thaliana</i>. PastDB contains AS events (including exon skipping, alternative 5' and 3' splice sites and retained introns). AS event identification and sequence inclusion level quantification in RNA-seq samples have been performed with [https://github.com/vastgroup/vast-tools <i>vast-tools</i>]. |
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In addition to AS inclusion levels, PastDB provides general information about the AS events, including genomic and sequence context, impact on the reading frame, overlap with protein domains and disordered regions and primers for AS event validation through RT-PCR. Moreover, it also provides measures of Gene Expression, using the cRPKM metric. | In addition to AS inclusion levels, PastDB provides general information about the AS events, including genomic and sequence context, impact on the reading frame, overlap with protein domains and disordered regions and primers for AS event validation through RT-PCR. Moreover, it also provides measures of Gene Expression, using the cRPKM metric. | ||
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If you see an AS event that you find inconsistent, or you have any questions, comments or suggestions about the database, please do not hesitate to e-mail us to [mailto:vastdb@googlegroups.com vastdb@googlegroups.com]. | If you see an AS event that you find inconsistent, or you have any questions, comments or suggestions about the database, please do not hesitate to e-mail us to [mailto:vastdb@googlegroups.com vastdb@googlegroups.com]. | ||
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| + | How to cite: if you use data from PastDB, please cite our paper in [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02258-y Genome Biology]: | ||
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| + | Martín, G., Márquez, Y., Duque, P., Irimia, M. (2021). Alternative splicing landscapes in <i>Arabidopsis thaliana</i> across tissues and stress conditions highlight major functional differences with animals. Genome Biol, 22:35. | ||
Latest revision as of 11:21, 17 January 2021
PastDB is a database of Alternative Splicing (AS) profiles across multiple tissues and environmental conditions of Arabidopsis thaliana. PastDB contains AS events (including exon skipping, alternative 5' and 3' splice sites and retained introns). AS event identification and sequence inclusion level quantification in RNA-seq samples have been performed with vast-tools.
In addition to AS inclusion levels, PastDB provides general information about the AS events, including genomic and sequence context, impact on the reading frame, overlap with protein domains and disordered regions and primers for AS event validation through RT-PCR. Moreover, it also provides measures of Gene Expression, using the cRPKM metric.
If you see an AS event that you find inconsistent, or you have any questions, comments or suggestions about the database, please do not hesitate to e-mail us to vastdb@googlegroups.com.
How to cite: if you use data from PastDB, please cite our paper in Genome Biology:
Martín, G., Márquez, Y., Duque, P., Irimia, M. (2021). Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals. Genome Biol, 22:35.