Genome BioInformatics Research Lab
Help
|
News
|
People
|
Research
|
Software
|
Publications
|
Links
Resources & Datasets
|
Gene Predictions
|
Seminars & Courses
IMIM
UPF
CRG
GRIB
Resources & Datasets
Mulitple-species conservation
Multiple-species conservation vs evolvability: case study of splicing regulators
Contents
Abstract
Methods
Data
Results
ABSTRACT
Between-species conservation as a source of information on functionality:
METHODS
Naive conservation measure versus Phylogenetic conservation
DATA
Multiple alignments of the orthologous exon sequences
set of 8775 constitutive exon
pruned set of exons of 8583
exons with weak 3' splice site
(
README
)
exons with strong 3' splice site
exons with weak 5' splice site
exons with strong 5' splice site
Splice site partitions of the orthologous exon alignments
Position weight matrices for scoring the SS (PWMs)
3' SS
5' SS
Putative Exonic Splicing Regulator Sequences
regulatory pentamers ESEs
``training neutral'' hexamers
``testing neutral'' hexamers
Tree inference
Exon alignments with the positions extracted
random samples
ESE
Phylogenetic trees for the data sets
weak 3'SS
strong 3'SS
weak 5'SS
strong 5'SS
all synonymous genomic positions
wobble positions excluding its subset covered by the ESEs
Ranking of all pentamers according to the preservation scores across the multiple-species alignment (increasing order)
scores attained by the Naive-Conservation measure (human-as-reference base comparison)
...corresponding motifs
scores attained by the Phylo-Conservation measure (including the phylogenetic information)
...corresponding motifs
pentamers removed from the analysis for the insufficient data (few occurrences)
RESULTS
results
....
Disclaimer
webmaster