Supplementary material for "Fastcompare: a simple and efficient approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation"

Authors are Olivier Elemento and Saeed Tavazoie. They can be contacted at elemento AT princeton.edu and tavazoie AT genomics.princeton.edu


Distributed programs and scripts :

- download the full distribution (binaries and source) for Linux [ zip ], Windows [ zip ].

- download individual plateform-specific programs (written in the C language)


 Linux Windows Source
fastcompare fastcompare_LINUX.bin fastcompare_WIN.exe fastcompare.c
do_fastcompare_conserved_set do_fastcompare_conserved_set_LINUX.bin do_fastcompare_conserved_set_WIN.exe do_fastcompare_conserved_set.c
do_fastcompare_coconservation do_fastcompare_coconservation_LINUX.bin do_fastcompare_coconservation_WIN.exe do_fastcompare_coconservation.c

- k-mer lists

5-mers    DNA    RNA
6-mers    DNA    RNA
7-mers    DNA    RNA
8-mers    DNA    RNA
9-mers    DNA    RNA
10-mers  DNA    RNA

- download pcre.dll for the above Windows binaries (not used in fastcompare.exe)

- download individual plateform-independent Perl scripts

do_fastcompare_alignment

do_fastcompare_randomization

- download the following Perl modules (required for the above Perl scripts): 

Sets.pm 
Table.pm
ClustalW.pm
Fasta.pm
Sequence.pm


- download the following external packages: 

ClustalW:     EBI
Perl:             ActivePerl for Windows


Additional scripts

- genome annotation using orthologous protein sequences
- orthology determination using best reciprocal BLAST hits 
- upstream region extraction from genome and gene coordinate files
- determing which k-mer match the 5' extremity of a list of miRNAs