Either (1) or (2) is required for Spliceman 2. If the format that the user inputs is not correct or if there are any variants in the input that fall outside gene boundaries the program will return appropriate error message to the user.
Spliceman can handle two different input formats. Here, you can input at most 5 mutations. Each mutation has to be in a single line and include: chromosome, variant_position(1-based), reference_allele, and alternative_allele; space separated, as shown in the placeholder. Spliceman 2 only accepts GRCh37 assembly coordinates.
Alternatively, you can click on Load Sample Data button (6). That will input two sample variants in the text field that will show the correctly formatted input. To process that sample just follow with a click on (3) Process Sequences Button.
Spliceman can handle two different input formats. Here, you can upload .vcf file that is limited by size to 10MB. Detailed description of .vcf format can be found HERE. Spliceman 2 only accepts GRCh37 assembly coordinates.
This button is submitting the form for evaluation by the Spliceman 2 algorithm.
This button clears the form from any input values.
Now offers users the opportunity to recommend variants for submission to our high-throughput in vitro and in vivo splicing assays. If users select this option, they are asked to opt-out of the default permission (i.e., anonymous users and private data) and register on our internal portal.
Load two sample variants in the text field that will show the correctly formatted input.
Visualization of the locations – within exons and introns – of analyzed sequence variants. Variants are shown as red vertical lines, exons are blue rectangles introns are black horizontal lines.
Table of prediction of which RNA-binding proteins are mostly disrupted by the variant. The table also lists location of each processed variant.
Predicted effects on splicing of the pre-mRNA transcript of each variant. The reported value is the absolute value of log base 10 of p-value. For example, a value greater than 1.3 means p-value less than 0.05 that the variant is disrupting splicing. Values over 1.3 are colored red; values less than 1.3 are blue. The user can mouse-over the bars to see the exact value for each variant. The output also includes location of each variant as a coordinate as well as how far it is from a particular splice site.
If you use this tool in research, please cite:
Lim K. H. and Fairbrother W. G. (2012). "Spliceman--a computational web server that predicts sequence variations in pre-mRNA splicing." Bioinformatics 28(7): 1031-1032. Bioinformatics DOI: 10.1093/bioinformatics/bts074