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http://www.jiffynet.org/

Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species.

Proper citation: JiffyNet (RRID:SCR_011954) Copy   

•   Source: SciCrunch Registry

http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm

A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.

Proper citation: ArrayMiner (RRID:SCR_011955) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirplant/

A user-friendly plant miRNA prediction tool.

Proper citation: miRPlant (RRID:SCR_012105) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/slidesort-bpr/

Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.

Proper citation: SlideSort-BPR (RRID:SCR_012079) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.jku.at/software/fabia/fabia.html

A model-based technique for biclustering that is clustering rows and columns simultaneously.

Proper citation: FABIA (RRID:SCR_012002) Copy   

•   Source: SciCrunch Registry

http://mfpaq.sourceforge.net/

Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).

Proper citation: MFPaQ (RRID:SCR_012049) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/multiplierz/

An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.

Proper citation: multiplierz (RRID:SCR_012058) Copy   

•   Source: SciCrunch Registry

http://www.computationalbioenergy.org/meta-storms.html

Optimized GPU-based software to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples.

Proper citation: GPU-Meta-Storms (RRID:SCR_012029) Copy   

•   Source: SciCrunch Registry

http://opencobra.sourceforge.net/openCOBRA/Welcome.html

Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.

Proper citation: COBRApy (RRID:SCR_012096) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/netcoffee/

A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.

Proper citation: NetCoffee (RRID:SCR_012095) Copy   

•   Source: SciCrunch Registry

http://mothra.ornl.gov/cgi-bin/cat/cat.cgi

A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CAT (RRID:SCR_008421) Copy   

•   Source: SciCrunch Registry

http://go.princeton.edu/cgi-bin/GOTermFinder

The Generic GO Term Finder finds the significant GO terms shared among a list of genes from an organism, displaying the results in a table and as a graph (showing the terms and their ancestry). The user may optionally provide background information or a custom gene association file or filter evidence codes. This tool is capable of batch processing multiple queries at once. GO::TermFinder comprises a set of object-oriented Perl modules GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script. This implementation, developed at the Lewis-Sigler Institute at Princeton, depends on the GO-TermFinder software written by Gavin Sherlock and Shuai Weng at Stanford University and the GO:View module written by Shuai Weng. It is made publicly available through the GMOD project. The full source code and documentation for GO:TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Generic GO Term Finder (RRID:SCR_008870) Copy   

•   Source: SciCrunch Registry

http://plantgrn.noble.org/LegumeIP/

LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression.

Proper citation: LegumeIP (RRID:SCR_008906) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gma

Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure.

Proper citation: GMA (RRID:SCR_009212) Copy   

•   Source: SciCrunch Registry

http://clipserve.clip.ubc.ca/topfind

An integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases. It lists more than 120,000 N- and C-termini and almost 10,000 cleavages. TopFIND is a resource for comprehensive coverage of protein N- and C-termini discovered by all available in silico, in vitro as well as in vivo methodologies. It makes use of existing knowledge by seamless integration of data from UniProt and MEROPS and provides access to new data from community submission and manual literature curating. It renders modifications of protein termini, such as acetylation and citrulination, easily accessible and searchable and provides the means to identify and analyse extend and distribution of terminal modifications across a protein. The data is presented to the user with a strong emphasis on the relation to curated background information and underlying evidence that led to the observation of a terminus, its modification or proteolytic cleavage. In brief the protein information, its domain structure, protein termini, terminus modifications and proteolytic processing of and by other proteins is listed. All information is accompanied by metadata like its original source, method of identification, confidence measurement or related publication. A positional cross correlation evaluation matches termini and cleavage sites with protein features (such as amino acid variants) and domains to highlight potential effects and dependencies in a unique way. Also, a network view of all proteins showing their functional dependency as protease, substrate or protease inhibitor tied in with protein interactions is provided for the easy evaluation of network wide effects. A powerful yet user friendly filtering mechanism allows the presented data to be filtered based on parameters like methodology used, in vivo relevance, confidence or data source (e.g. limited to a single laboratory or publication). This provides means to assess physiological relevant data and to deduce functional information and hypotheses relevant to the bench scientist. TopFIND PROVIDES: * Integration of protein termini with proteolytic processing and protein features * Displays proteases and substrates within their protease web including detailed evidence information * Fully supports the Human Proteome Project through search by chromosome location CONTRIBUTE * Submit your N- or C-termini datasets * Contribute information on protein cleavages * Provide detailed experimental description, sample information and raw data

Proper citation: TopFIND (RRID:SCR_008918) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.fccc.edu/software/OpenSource/FGDP/FGDP.shtml

A Java-based, Microarray or Genechip data analysis system.

Proper citation: FGDP (RRID:SCR_008910) Copy   

•   Source: SciCrunch Registry

http://hymenopteragenome.org/beebase/

Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page.

Proper citation: BeeBase (RRID:SCR_008966) Copy   

•   Source: SciCrunch Registry

http://pages.stat.wisc.edu/~yandell/qtl/software/qtlbim/

Software library for QTL Bayesian Interval Mapping that provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits. (entry from Genetic Analysis Software)

Proper citation: R/QTLBIM (RRID:SCR_009375) Copy   

•   Source: SciCrunch Registry

https://github.com/lpantano/seqbuster

Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells.

Proper citation: SeqBuster (RRID:SCR_009616) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/MACH/download/

QTL analysis based on imputed dosages/posterior_probabilities.

Proper citation: MACH (RRID:SCR_009621) Copy   

•   Source: SciCrunch Registry