Ases :: Alternative Splicing Evolution Server

Gene Name or Ensembl Stable ID (ENS... recommended)

Species

PhyloSofS

PhyloSofS perform the phylogenetic reconstruction for the transcripts, but it can take several hours.

List of species
binomial nomenclature
use commas or line returns as separators. If the species list is empty, all the available species with annotated orthologs in Ensembl will be used (slow).

ThorAxe Orthology detection between exons and Evolutionary Splicing Graph construction

Maximum Transcript Support Level

Percent Identity for exon clustering

PhyloSofS Transcripts' phylogenies reconstruction

Birth cost

Death cost

Mutation cost

ThorAxe

Ensembl data

Orthology

Orthology relationship to use: 1:1, 1:n or m:n. It is possible to get more genes and transcripts by allowing for 1:n or m:n orthologs. However, ThorAxe can not ensure that the s-exons contain only orthologous exonic regions under that setup.

General

Minimum exon length

Exons shorter than this value will not be considered in the clustering step.

Pairwise alignment

Coverage

Minimum required coverage for the shortest exon in the pair.

Gap open penalty

Penalty for a gap opening.

Gap extension penalty

Penalty for gap extensions.

Multiple Sequence Alignment

Padding length

Length of padding (symbol X) separating sub-exons that never co-occur in a transcript.

Rescue unaligned sub-exons

Try and re-assign the sub-exons that do not align against any other sequence in the MSA to another cluster (disabled by default).

No stretch shift

Turn off the refinement of s-exons through shifting of the very small sequence stretches isolated by gaps (enabled by default).

No disintegration

Turn off the refinement of s-exons through disintegration of the 1-column s-exons (enabled by default).

Alternative splicing event detection

Minimum species number

Minimum number of supporting species required for a path to be considered.

Minimum transcript number

Minimum number of supporting transcripts required for a path to be considered.

Canonical transcript criteria

List of transcript features (column names in the path_table) separated by commas or line returns used to sort the transcripts (rows in the path_table).

PhyloSofS

Number of iterations

Number of phylogenetic forest structures sampled and evaluated by the algorithm.

No pruning

Turn off the removal of s-exons that appear in only one transcript (enabled by default).

E-mail Optional. We will e-mail you when the computation is done. Note that depending on the demand, the calculation may take more than an hour to complete.