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https://jmorp.megabank.tohoku.ac.jp/

Japanese multi omics reference panel. Provides multidimensional approach to diversity of Japanese population. Public database for plasma metabolome and proteome analyses. Updated to metabolome, genome, transcriptome, metagenome, number of samples, analysis methods of each dataset, expanding links between each layer and links between hierarchies.

Proper citation: jMORP (RRID:SCR_024755) Copy   

•   Source: SciCrunch Registry

http://www.ngfn.de/en/start.html

The program of medical genome research is a large-scale biomedical research project which extends the national genome research net (NGFN) and will be funded by the federal ministry of education and research (BMBF) from 2008-2013. Currently the program includes two fields: * Research ** NGFN-Plus: With the aim on combating diseases that are central to health policy, several hundred researchers are systematically investigating the complex molecular interactions of the human body. They are organized in 26 Integrated Genome Research Networks. * Application ** NGFN-Transfer: The rapid transfer of results from medical genome research into medical and industrial application is the aim of the scientists from research institutes and biomedical enterprises that cooperate in eight Innovation Alliances. AREAS OF DISEASE * Cardiovascular disease * Cancer * Neuronal diseases * Infections and Inflammations * Environmental factors

Proper citation: National Genome Research Network (RRID:SCR_006626) Copy   

•   Source: SciCrunch Registry

http://icebox.lbl.gov:8080/ApolloWebDemo/jbrowse/

WebApollo is an extensible web-based sequence annotation editor for community annotation. No software download is required and the annotations are saved to a centralized database with real-time annotation updating. (The edit server mediates annotation changes made by multiple users.) The Web based client uses JBrowse, is fast and highly interactive. WebApollo accesses many types of genomic data including access to public data from UCSC, Ensembl, and GMOD Chado databases. Source code (BSD License) * Client source code: https://github.com/berkeleybop/jbrowse * Annotation editing engine: http://code.google.com/p/apollo-web * Data model and I/O layer: http://code.google.com/p/gbol * Trellis server code: http://code.google.com/p/genomancer

Proper citation: WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation (RRID:SCR_005321) Copy   

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https://github.com/TransDecoder/TransDecoder

Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.

Proper citation: TransDecoder (RRID:SCR_017647) Copy   

•   Source: SciCrunch Registry

https://github.com/shendurelab/LACHESIS

Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies.

Proper citation: LACHESIS (RRID:SCR_017644) Copy   

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https://bitbucket.org/mroachawri/purge_haplotigs/src

Pipeline for reassigning primary contigs that should be labelled as haplotigs. Used for third generation sequencing based assemblies to automate reassignment of allelic contigs, and to assist in manual curation of genome assemblies.

Proper citation: Purge_haplotigs (RRID:SCR_017616) Copy   

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https://www.sanger.ac.uk/science/tools/reapr

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy   

•   Source: SciCrunch Registry

https://openwetware.org/wiki/HughesLab:JTK_Cycle

Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets.

Proper citation: JTK_CYCLE (RRID:SCR_017962) Copy   

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https://chlorobox.mpimp-golm.mpg.de/geseq.html

Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.

Proper citation: GeSeq (RRID:SCR_017336) Copy   

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https://github.com/Brazelton-Lab/seq-annot

Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.

Proper citation: seq-annot (RRID:SCR_018731) Copy   

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https://github.com/lufuhao/GeneSyntenyPipeline

Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome.

Proper citation: GeneSyntenyPipeline (RRID:SCR_018198) Copy   

•   Source: SciCrunch Registry

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information.

Proper citation: CustomCDF (RRID:SCR_018527) Copy   

•   Source: SciCrunch Registry

http://seqant.genetics.emory.edu/

A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest.

Proper citation: SeqAnt (RRID:SCR_005186) Copy   

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http://compbio.cs.brown.edu/projects/gasv/

Software tool combining both paired read and read depth signals into probabilistic model which can analyze multiple alignments of reads. Used to find structural variation in both normal and cancer genomes using data from variety of next-generation sequencing platforms. Used to predict structural variants directly from aligned reads in SAM/BAM format.Combines read depth information along with discordant paired read mappings into single probabilistic model two common signals of structural variation. When multiple alignments of read are given, GASVPro utilizes Markov Chain Monte Carlo procedure to sample over the space of possible alignments.

Proper citation: GASVPro (RRID:SCR_005259) Copy   

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http://bejerano.stanford.edu/prism/public/html/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PRISM (Stanford database) (RRID:SCR_005375) Copy   

•   Source: SciCrunch Registry

http://www.yandell-lab.org/software/mwas.html

The MAKER Web Annotation Service (MWAS) is an easily configurable web-accessible genome annotation pipeline. It''''s purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence (i.e. BAC clones, small whole genomes, preliminary sequencing data, etc.) to independently annotate and analyze their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline MAKER, and users who wish to annotate larger datasets and whole genomes are free to download MAKER for use on their own systems. MWAS identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MWAS can also automatically train popular gene prediction algorithms for use on new genomes for which pre-existing information is limited. MAKER is a member of the Generic Model Organism Database (GMOD) project and output produced by this site can be directly used with other GMOD tools. Annotations can be directly viewed online by the user via GBrowse, JBrowse, and Apollo, or they can be downloaded for local analysis and integration into a genome database. MWAS also supplies summary statistics on sequence features via the Sequence Ontology tool SOBA. MWAS should prove especially useful for emerging model organism genome projects with minimal bioinformatics expertise and computer resources, since a user can produce final genome annotations without having to install and configure any software locally.

Proper citation: MAKER Web Annotation Service (RRID:SCR_005318) Copy   

•   Source: SciCrunch Registry

http://gds.nih.gov/

NIH established expectations for sharing data obtained through NIH-funded genome-wide association studies (GWAS) with the implementation of the GWAS Policy. Information and resources related to the GWAS Policy can be found on this website.

Proper citation: Genomic Datasharing (RRID:SCR_005233) Copy   

•   Source: SciCrunch Registry

http://microbesonline.org/

MicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

Proper citation: MicrobesOnline (RRID:SCR_005507) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/ws/ws.php?entry=BLASTatlas

The BLASTatlas is a tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms using either blastp, blastn, tblastn, or blastx. DNA structural information is also included in the atlas to visualize the DNA chromosomal context of regions. Additional information can be added to these plots. The tool is SOAP compliant and WSDL (web services description language) files are available with programming examples available in Perl. The resolution is per-residue or per nucleotide depending on the regime of the blast search: For each annotation in the reference genome, the best hit in the database genome is found using one of the above algorithms. Each matching or mismatching residue/nucleotide of the best hit (based on BLAST score) is then mapped back to the genome sequence, using the coordinates provided in the annotations. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence enabling automation of repeated tasks. This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set.

Proper citation: BLASTatlas - Mapping of whole genome homology (RRID:SCR_005891) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/pfa/iprscan/

Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service.

Proper citation: InterProScan (RRID:SCR_005829) Copy   

•   Source: SciCrunch Registry