SpliceS: Fast scanner for conserved splice sites in gene homologs across species

SpliceS is a tool to identify splice sites conserved across multiple species, facialiating primer design in transcript homologs of novel species. Developed by the Center for Research Informatics (CRI) bioinformatics core at the University of Chicago.

The pipeline is implemented in

• Perl

Download

To download SpliceS, please use git to download the most recent version.

$ git clone https://github.com/riyuebao/SpliceS.git

System Requirement

• SpilceS requires perl 5.18.1 or higher.
• To visualize the sequences in Fasta format or generate alignment: MEGA
• To quickly map sequence to the genome and visualize the gene model: BLAT.

Usage

For a description of available command-line options and their defaults, run:

$ ./SpliceS.pl

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Copyright (c) 2016 Center for Research Informatics, University of Chicago

Usage: SpliceS.pl [OPTIONS]
Vesion: 0.1.0

Options:
 [-i|--input]     : Input sequence file. Fasta format.
                    Sequence header format must contain three fields,
                    separated by [|].  No space allowed.
                    For example: >gene_symbol|transcript_accessionID|species
                    [species] must be
                    rn or rn6; mm or mm10; hg or hg38.
             Note : All three homolog sequences are required (rn, mm, hg).
 [-o|--output]    : Output file prefix. Default is "$input.out".
 [-rn|--rat]      : Rat RefSeq gene annotation. refFlat format.
 [-mm|--mouse]    : Mouse RefSeq gene annotation. refFlat format.
 [-hg|--human]    : Human RefSeq gene annotation. refFlat format.
             Note : All three annotation files are required (rn, mm, hg).

Three output files will be generated:
 $output.seq.txt : Non-gapped transcript sequence with splice site labeled.
 $output.gene_model.txt: Gene model information of known species.
 $output.splice_pos.txt: Splice position information of the gene homologs.

Example: SpliceS.pl \
         -i KiSS1.hamster_RNAseq.alignment.fasta \
         -rn ../data/rn6.refFlat.txt \
         -mm ../data/mm10.refFlat.txt \
         -hg ../data/hg38.refFlat.txt

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Quick Start

To gain the first look into how to tool works, we provide sample data and scripts for a quick start demo.

In directory example/

• KiSS1.hamster_RNAseq.alignment.fasta Transcript sequence alignment
• run_example.sh Example commands to run the tool
• KiSS1.hamster_RNAseq.alignment.fasta.out files Output files generated by the commands
• run_example.log Log file after running the commands

To regenerate the output files, run:

cd example
./run_example.sh

Contact

Questions and comments? Please contact Riyue Bao at <rbao at uchicago dot edu>, or post on Issues.

Release

• Version 0.1.0 2016-06-28

TODO

• Add alignment function
• Add vsualization