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PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small, command line tool to designate and analyze PICS (Schilling et al., Nat. Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be concurrently used to generate cleavage specificity visualizations like the iceLogo (https://iomics.ugent.be/icelogoserver/create).

---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid...

**** This page is not used for this project any longer. *** Please update your bookmarks and go to https://github.com/UUPharmacometrics/PsN

BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball.

A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/

Ours organization website GCModeller.org is coming online soon! Shoal Shell is the sub project for the "genome-in-code"(http://code.google.com/p/genome-in-code/) virtual cell modelling project of the bacteria Xcc 8004. Shoal Shell aim at provide the modelling tool and the debugging tool for the GCModeller virtual cell modelling, And from the extendible library package, shoal shell can manage to accomplish the entire modelling job for any other bacteria species. Shoal Shell Project...

NOTE: TransGeneScan is migrated to Github (https://github.com/COL-IU/TransGeneScan). TransGeneScan is no longer maintained in SourceForge. Please find the latest version in Github. TransGeneScan is a gene finding tool for Metatranscriptomic sequences. TransGeneScan incorporates strand-specic hidden states, representing coding sequences in sense and anti-sense strands on transcripts in a Hidden Markov Model similar to the one used in FragGeneScan (http://fraggenescan.sourceforge.net/), and can predict a sense transcript containing one or multiple genes (in an operon) or an antisense transcript.