The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence.
BACKGROUND
Some mutations in the internal regions of exons occur within splicing enhancers and silencers, influencing the pattern of alternative splicing in the corresponding genes. To understand how these sequence changes affect splicing, we created a database of these mutations.


RESULTS
The Alternative Splicing Mutation Database (ASMD) serves as a repository for all exonic mutations not associated with splicing junctions that measurably change the pattern of alternative splicing. In this initial published release (version 1.2), only human sequences are present, but the ASMD will grow to include other organisms, (see Availability and requirements section for the ASMD web address).This relational database allows users to investigate connections between mutations and features of the surrounding sequences, including flanking sequences, RNA secondary structures and strengths of splice junctions. Splicing effects of the mutations are quantified by the relative presence of alternative mRNA isoforms with and without a given mutation. This measure is further categorized by the accuracy of the experimental methods employed. The database currently contains 170 mutations in 66 exons, yet these numbers increase regularly.We developed an algorithm to derive a table of oligonucleotide Splicing Potential (SP) values from the ASMD dataset. We present the SP concept and tools in detail in our corresponding article.


CONCLUSIONS
The current data set demonstrates that mutations affecting splicing are located throughout exons and might be enriched within local RNA secondary structures. Exons from the ASMD have below average splicing junction strength scores, but the difference is small and is judged not to be significant.
Bechtel
Jason M
JM
Program in Bioinformatics and Proteomics/Genomics, University of Toledo Health Science Campus, Toledo, Ohio 43614, USA. jason.bechtel@utoledo.edu
Rajesh
Preeti
P
Ilikchyan
Irina
I
Deng
Ying
Y
Mishra
Pankaj K
PK
Wang
Qi
Q
Wu
Xiaochun
X
Afonin
Kirill A
KA
Grose
William E
WE
Wang
Ye
Y
Khuder
Sadik
S
Fedorov
Alexei
A