BIOINFORMATICS APPLICATIONS NOTE
Vol. 28 no. 7 2012, pages 1031–1032
Spliceman—a computational web server that predicts sequence
variations in pre-mRNA splicing
Kian Huat Lim1and William Guy Fairbrother1,2,∗
1Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02903 and
2Center of Computational Molecular Biology, Brown University, Providence, RI 02012, USA
Associate Editor: Ivo Hofacker
Advance Access publication February 10, 2012
Summary: It was previously demonstrated that splicing elements
are positional dependent. We exploited this relationship between
location and function by comparing positional distributions between
all possible 4096 hexamers around a database of human splice sites.
The distance measure used in this study found point mutations
that produced higher distances disrupted splicing, whereas point
mutations with smaller distances generally had no effect on splicing.
Reasoning the idea that functional splicing elements have signature
positional distributions around constitutively spliced exons, we
introduce Spliceman—an online tool that predicts how likely distant
mutations around annotated splice sites were to disrupt splicing.
Spliceman takes a set of DNA sequences with point mutations and
returns a ranked list to predict the effects of point mutations on pre-
mRNA splicing. The current implementation included the analyses of
11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken,
guinea pig, frog and zebrafish.
Availability: Freely available on the web at http://fairbrother.biomed
Received on June 23, 2011; revised on January 19, 2012; accepted
on January 25, 2012
Pre-mRNA splicing is an important regulatory step in gene
expression pathway: introns are removed and exons are joined
to form mRNA. The splicing process is performed by the
spliceosome, a macromolecular ribonucleoprotein complex that
rivals the ribosome in size and complexity. The intricate assembly
of the spliceosome is guided by the consensus splice site sequences
(i.e. branch point, polypyrimidine tract, 3?and 5?splice sites)
and a family of subsidiary elements known as intron and exon
splicing enhancers and silencers. Estimates of the fraction of disease
mutations that cause aberrant splicing had been reported to range
from 15% (Stenson et al., 2003) to 62% (Lopez-Bigas et al., 2005).
In a previous study (Lim et al., 2011), we demonstrated that
splicing elements had signature positional distributions around
constitutively spliced exons—they were abundant where they
functioned positively and rare when they were inhibitory. We
captured these positional properties for hexamers with the L1
distance metric (Section 2) and used it to cluster positional
distributions of all possible 4096 hexamers around human splice
∗To whom correspondence should be addressed.
sites. In addition to recognizing consensus splice site sequences, our
splicing enhancers and silencers. Experimental verifications of the
computational results strongly indicated the power of this method to
be predictive. Specifically, we found point mutations that produced
whereas point mutations with small distances generally had no
affect on splicing. To facilitate the analysis of splicing mutations,
we present Spliceman—an online tool that predicts how likely a
found in the consensus splice donor and acceptor sites can often be
predicted with high accuracy, Spliceman also excludes splice sites
positions in order to predict distant splicing enhancers and silencers.
The computational engine and web interface were developed in Perl and
with the use of Bioperl toolkit (Stajicn et al., 2002). The tool was designed
to accept a set of DNA sequences with mutational data in FASTA format.
Design and implementation
Exon database of each species was built from Refseq annotations of the
following assemblies stored at the UCSC Table Browser (Karolchik et al.,
2004): human (hg18 and hg19), chimp (panTro3), rhesus (rheMac2), mouse
(mm9), rat (rn4), dog (canFam2), cat (felCat4), chicken (galGal3), guinea
pig (cavPor3), frog (xenTro2) and zebrafish (danRer7). Duplicated entries
were removed, and each sequence was divided into two distinct regions:
upstream intron (up to 200 intronic and 100 exonic nucleotides of 3?ss) and
downstream intron (up to 200 intronic and 100 exonic nucleotides of 5?ss).
Therefore, each sequence in the exon database contained at most 600nt.
In the case where intronic or exonic sequence length was <400 or 200nt,
respectively, the sequences were equally divided and each half was assigned
to its nearest splice site.
Preparation of exon databases
Step (1) Selecting word size and generating feature vectors: RNA binding
proteins typically contain one to four RNArecognition motif domains so that
motifs recovered are expected to be of heterogeneous length. Our analysis of
prior SELEX studies indicated that RNAbinding proteins recognized motifs
between the length of 6–10nt (Lim et al., 2011). Previous implementations
of dictionary methods also illustrated how a smaller word size choice was
generally self-correcting (Fairbrother et al., 2002; Zhang and Chasin 2004).
For these reasons, as well as computation efficiency, we selected hexamers
for the analysis presented here. For each hexamer, the counting algorithm
traversed through the exon database and recorded the occurrences of that
hexamer at 600 different positions relative to splice sites. Repeated this
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procedure for all hexamers generated 4096 feature vectors. Each feature
locations relative to splice sites. Since overlapping occurrences of internally
repeated words can occur more frequently than complex words, overlapping
occurrences of any words were counted as a single occurrence in a window
of 11. For example, a run of 11A’s (i.e.AAAAAAAAAAA) was counted as
single occurrence at the position where it was first observed.
Step (2) Quantifying similarities and differences between feature vectors
by computing L1 distance metric: this tool used the L1 distance metric to
quantify the ‘closeness’between two feature vectors. An obvious choice for
distance metric is the Euclidean or L2 distance; however, the sharp peaks
created by the splice site hexamers themselves dominated the comparison
and prevented the detection of more subtle signals. This was remedied by
using the Manhattan distance, also referred to as the city block distance or
simply L1 distance. L1 distance was calculated as the sum of the absolute
differences in feature vectors at each of the 600 positions. The higher the L1
distance between two hexamers (i.e. wild type versus point mutation), the
greater the differences are between them, thereby the mutation is predicted to
be more likely to alter splicing. In order to facilitate in the analyses of distant
splicing elements, Spliceman also calculates L1 distance metric by masking
out splice sites positions (e.g. 20 intronic positions upstream and 5 exonic
positions downstream of the 3?splice site; 5 exonic positions upstream and
8 positions downstream of the 5?splice site).
Step (3) Calculating percentile ranks for L1 distances: this method binned
all possible L1 distances into 100 equal intervals and assigned each L1
distance to its corresponding bin. For instance, comparisons between two
hexamers that resulted in low L1 distances would be assigned with low
Spliceman takes a set of DNA sequences with point mutations and
computes how likely these single nucleotide variants alter splicing
phenotypes. For each mutation given in the input form, the tool
reports the L1 distance and percentile rank that correspond to the
given mutation. This is the rank that the tool uses to predict how
likely a mutation is to disrupt pre-mRNA splicing. The higher the
percentile rank, the more likely the point mutation is to disrupt
4RECEIVER OPERATING CHARACTERISTIC
We previously demonstrated the predictive power of the proposed
method by clustering hexamers into distinct groups based on
suggested that mutations with high L1 distances altered splicing,
whereas mutations with low L1 distances generally had no affect on
splicing. To further analyze the predictive power of this method, we
computed receiver operating characteristic (ROC) curve statistics
using a binary classifier (‘0’ corresponds to true positive samples
derived from a set of 1987 confirmed splicing mutations found in
false positive samples constructed from a set of simulated mutations
using equal rates of transversions and transitions). ROC statistics
annotated human splice sites (upstream 3?splice site introns, exons
and downstream 5?splice site introns). Since splice site sequences
can often be predicted with high accuracy, we removed HGMD
Fig. 1. L1 distance metric is predictive of distant splicing mutations. ROC
curve analysis using HGMD splicing mutations to compare L1 distances in
three distinct regions around the annotated human splice sites. True positive
samples are derived from a total of 1987 HGMD splicing mutants found
outside of the donor and acceptor sites, and false positive samples are
constructed from simulated mutations using equal rates of transversions and
transitions. The exonic region is shown in green; upstream and downstream
introns are shown in blue and red, respectively.AUC, area under curve; C.I.,
mutations that were located in the consensus splice donor and
acceptor sites to measure the predictive power of this method
on distant splicing enhancers and silencers. The area under curve
measurements suggested our proposed method was predictive of
distant splicing mutations (Fig. 1).
Funding: The lab is funded by the National Institute of Health
Conflict of Interest: none declared.
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