SINE_Scan: an efficient tool to discover SINEs in genomic datasets
Prerequisites The following software tools/modules should be installed in your system:
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Perl and BioPerl Modules. All modules can be obtained from CPAN (http://search.cpan.org/).
(1). Statistics::Basic; (we have put this module into SINE_Scan subdirectory modules. The user does not need to install it)
(2). Parallel::ForkManager; (we have put this module into SINE_Scan subdirectory modules. The user does not need to install it)
(3). Bio::AlignIO;
(4). Bio::Align;
(5). Bio::PairwiseStatistics;
(6). Bio::SimpleAlign;
(7). Getopt::Long;
(8). File::Basename;
(9). Get::Sdt;
(10). Bio::SeqIO;
(11). Bio::Seq;
(12). Bio::Tools::Run::StandAloneBlast;
(13). Bio::SearchIO;
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Python 2.X
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SINE-Finder.py: The python script can be downloaded from http://www.plantcell.org/content/suppl/2011/08/29/tpc.111.088682.DC1/Supplemental_Data_Set_1-sine_finder.txt.
Installation and usage of SINE_Scan Here we walk through the whole installation and running process by showing an example of using SINE_Scan to analyse human chromosome 21. Detailed explanation can be found in the user guide.
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Download SINE_Scan v1.1.1 from Github and install it in a directory (Here we did analysis in a directory named /home/maohlzj/SINE_Scan-v1.1.1).
(1). Download SINE-Finder from Plant Cell website, rename the downloaded file as SINE-FINDER.py, and put it into /home/maohlzj
(2). Install SINE_Scan by typing:
a. cd /home/maohlzj/SINE_Scan-v1.1.1 b. perl SINE_Scan_Installer.pl -f /home/maohlzj/ncbi-blast-2.2.31+/bin/makeblastdb -b /home/maohlzj/ncbi-blast-2.2.31+/bin/blastn -c /home/maohlzj/cd-hit/cd-hit-est -e /home/maohlzj/EMBOSS-6.6.0/emboss/stretcher -M /home/maohlzj/muscle -l /home/maohlzj/bedtools2/bin/bedtools -a /home/maohlzj/sine_finder.py -
Analysis of human chr21
(1). Put human chromosome 21 (file name: chr21.fasta) in /home/maohlzj/SINE_Scan-v1.1.1
(2). Run SINE_Scan by typing: perl SINE_Scan_process.pl -s 123 -g chr21.fasta -d Chr21 -z Chr21 -o chr21 >Chr21.log