Field 2: <source>
Field 3: <feature>
AStalavista distinguishes variations of the exon-intron structure into different classes, each one with a specific GTF feature.
| Feature | Description |
|---|---|
| as_event | An Alternative Splicing event compliant with the definition given in Sammeth et al. (2008). |
| ds_event | Additional Splicing event. For a definition, see here. |
| vs_event |
Field 6: <score>
AStalavista adapts a score developed by Sugnet et al. (2004), see function confidence in their program altSplice. The goal is to assign a higher score to events where all variants are supported by many transcript, and a lower score, when only the number of variants with strong transcript support. The AStalavista score for events with an arbitrary dimension $d \geq 2$ is
(1)with $sum_i^d |\mathit{support}$ being the total number of transcript that support an event, $\mathit{non-supporting_{event}}}$ the number of transcripts that overlap the event, but do not support either variant, and $\mathit{non-supporting_{event}}$ the difference between the support of two variants $i,j$ in the event. Therefore, larger scores are higher confident, but they usually range between 1-2.
Field 8: <frame>
No adaption currently available.
Field 9- <attributes>
For describing the attributes of events, AStalavista uses the following attribute tags
| Attribute | since | Description |
|---|---|---|
| locus_id | 2.3 | Identifier for the splicing locus where the event is observed. |
| transcript_id | 1.0 | A ,'' (comma'') separated list, that shows for each variant the list of transcript_id names from $\geq 1$ spliceforms that support the variant. Multiple transcript_id strings that support the same variant are separated by a /'' (dash''). |
| structure | 1.0 | The alternative splicing code (AS code) that describes qualitatively the exon-intron structure of the event as described in Sammeth et al. (2008). Variants are again seperated by ,'' (comma'') . |
| splice_chain | 1.0 | A ,'' (comma'') separated list, that shows for each variant the list of variable sites. Each site is described by an Integer value according to its genomic location, and a symbol according to its biological role |
| flanks | 1.1 | Common sites that delimit the event, if they exist (see Internal and external events). |
| flanks | 1.1 | Common sites that delimit the event, if they exist. |
| dimension | 1.2 | The number of variants in the event, an _'' (underscore'') separator, followed by the numer of variants in the corresponding complete event (i.e., the corresponding bubble of the splicing graph. |
| degree | 1.0 | The number of variable sites in the event. |
