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http://fatcat.burnham.org/

Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FATCAT (RRID:SCR_014631) Copy   

•   Source: SciCrunch Registry

https://github.com/Mangul-Lab-USC/telescope

Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted.

Proper citation: Telescope (RRID:SCR_017626) Copy   

•   Source: SciCrunch Registry

https://github.com/Gaius-Augustus/BRAKER

Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction.

Proper citation: BRAKER (RRID:SCR_018964) Copy   

•   Source: SciCrunch Registry

http://www.genoscope.cns.fr/gmove

Software tool for genome annotation. Eukaryotic gene prediction tool focused on evidence supported by expressed sequences like transcripts and conserved proteins alignments. Can be used to reannotate genomes, to do comparative gene prediction and improve existing genome annotation. Can predict gene models with canonical and non-canonical splice sites.

Proper citation: Gmove (RRID:SCR_019132) Copy   

•   Source: SciCrunch Registry

http://mgc.nci.nih.gov/

NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).

Proper citation: Mammalian Gene Collection (RRID:SCR_007024) Copy   

•   Source: SciCrunch Registry

http://oufti.org/

Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions.

Proper citation: Oufti (RRID:SCR_016244) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/ProP/

Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.

Proper citation: ProP Server (RRID:SCR_014936) Copy   

•   Source: SciCrunch Registry

http://www.cprofiler.org/

Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.

Proper citation: Composition Profiler (RRID:SCR_014630) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/psa/genewise/

Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.

Proper citation: GeneWise (RRID:SCR_015054) Copy   

•   Source: SciCrunch Registry

http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/

Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally.

Proper citation: ChromImpute (RRID:SCR_023990) Copy   

•   Source: SciCrunch Registry

https://github.com/HadrienG/InSilicoSeq

Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.

Proper citation: InSilicoSeq (RRID:SCR_024041) Copy   

•   Source: SciCrunch Registry

https://github.com/fccoelho/epigrass

Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior.

Proper citation: Epigrass (RRID:SCR_024016) Copy   

•   Source: SciCrunch Registry

https://github.com/jnktsj/DNApi/

Software de novo adapter prediction algorithm for small RNA sequencing data.

Proper citation: DNApi (RRID:SCR_024009) Copy   

•   Source: SciCrunch Registry

https://www.teuniz.net/edfbrowser/

Open source, multiplatform, universal viewer, annotator and toolbox intended for time-series storage files like EEG, EMG, ECG, BioImpedance, etc.

Proper citation: EDFbrowser (RRID:SCR_024021) Copy   

•   Source: SciCrunch Registry

https://posit.co/products/open-source/shinyserver/

Open Source platform to host multiple Shiny applications on single server.

Proper citation: shiny-server (RRID:SCR_024334) Copy   

•   Source: SciCrunch Registry

https://www.tau.ac.il/~itaymay/cp/rate4site.html

Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins.

Proper citation: Rate4Site (RRID:SCR_024222) Copy   

•   Source: SciCrunch Registry

https://www.sofa-framework.org/

Open source software framework targeting at real-time simulation, with emphasis on medical simulation.

Proper citation: sofa-apps (RRID:SCR_024346) Copy   

•   Source: SciCrunch Registry

https://github.com/cbrueffer/tophat-recondition

Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat.

Proper citation: TopHat-Recondition (RRID:SCR_024383) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/surankco/

Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.

Proper citation: surankco (RRID:SCR_024355) Copy   

•   Source: SciCrunch Registry

http://blocks.fhcrc.org/codehop.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Service to design PCR primers from protein multiple sequence alignments. NOTICE: This version of CODEHOP is no longer maintained.

Proper citation: CODEHOP (RRID:SCR_002898) Copy   

•   Source: SciCrunch Registry