cdeboever3 / svm-bpfinder

A tool for mammalian U2 branch point prediction.

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SVM-BPfinder - A tool for mammalian BP prediction. 

Andre Corvelo and Eduardo Eyras | Regulatory Genomics @ Universitat Pompeu Fabra, Barcelona, Spain | 2010 

This tool is free for purpose of academic, non-commercial research. The software must not be further distributed without prior permission of the authors.

CONTACTS:
    acorvelo[at]gmail.com
    eduardo.eyras[at]upf.edu

WEB:
    http://regulatorygenomics.upf.edu/SVM_BP/

REFERENCE:
    "A. Corvelo, M. Hallegger, C.W.J. Smith, E. Eyras. Genome-wide Association between Branch Point Properties and Alternative Splicing. ... (2010)"   

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IMPORTANT:
    SVM_BP requires SVMlight, which can be downloaded at:
        http://download.joachims.org/svm_light/current/svm_light_linux.tar.gz 

    After downloading SVMlight, copy the 'svm_classify' executable to the SVM_BP 'SCRIPTS/' folder.

    Make sure you have permission to execute:
        1)'svm_bpfinder.py'
        2)'SCRIPTS/svm_getfeat.py'
        3)'SCRIPTS/svm_classify'  

    To know more about SVMlight, please visit http://svmlight.joachims.org/

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USAGE:

    ./svm_bpfinder.py input_file species slen
	
    input_file -> input file name. FASTA format only.
    species    -> Choose one from the following models: Hsap Ptro Mmul Mmus Rnor Cfam Btau 
    slen       -> SVM_BPfinder will scan the last [slen] bases of each sequence assuming they correspond to the 3' end of introns.
                  For sequences of length smaller than [slen], the entire sequence will be scanned.   

OUTPUT:
    Results are printed to STDOUT, tab delimited, one line per BP candidate. Header included.
    Output fields:
        seq_id - Sequence Identifier
        agez - AG dinucleotide Exclusion Zone length
        ss_dist - Distance to 3' splice site
        bp_seq - BP sequence (nonamer; from -5 to +3 relative to the BP adenine)
        bp_scr - BP sequence score using a variable order Markov model
        y_cont - Pyrimidine content between the BP adenine and the 3' splice site
        ppt_off - Polypyrimidine tract offset relative to the BP adenine
        ppt_len - Polypyrimidine tract length
        ppt_scr - Polypyrimidine tract score
        svm_scr - Final BP score using the SVM classifier
    
EXAMPLE:
    The command:

        ./svm_bpfinder.py introns.fa Hsap 300

    scans the 3'-most 300nts of every sequence contained in the FASTA file named 'intron.fa', using a human-specific model ('Hsap').   

NOTE:
    SVM_BPfinder works by calling two scripts/programs: 
        1)'SCRIPTS/svm_getfeat.py' - collects features 
        2)'SCRIPTS/svm_classify'   - scores candidate BPs
    This creates two files in the working directory, which are removed once the final results are displayed.

    In case it gets interrupted, these two files might be left on your system.  		 
	
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