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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://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://github.com/taborlab/FlowCal

Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.

Proper citation: FlowCal (RRID:SCR_018140) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://github.com/ComparativeGenomicsToolkit/hal/tree/master/synteny

Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment.

Proper citation: halSynteny (RRID:SCR_018127) Copy   

•   Source: SciCrunch Registry

http://regulondb.ccg.unam.mx/

Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.

Proper citation: RegulonDB (RRID:SCR_003499) Copy   

•   Source: SciCrunch Registry

http://www.nextprot.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2025. Human protein knowledge platform. Knowledge platform for human proteins selects and filters high throughput data pertinent to human proteins from UniProtKB. Extends UniProtKB/Swiss-Prot annotations for human proteins to include several new data types.

Proper citation: neXtProt (RRID:SCR_008911) Copy   

•   Source: SciCrunch Registry

http://www.bioguo.org/AnimalTFDB/

A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: AnimalTFDB (RRID:SCR_001624) Copy   

•   Source: SciCrunch Registry

http://www.pubgene.org/

It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate.

Proper citation: PubGene (RRID:SCR_002119) Copy   

•   Source: SciCrunch Registry

http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/

Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.

Proper citation: COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) Copy   

•   Source: SciCrunch Registry

http://pallab.serc.iisc.ernet.in/gester/

Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed.

Proper citation: WebGeSTer DB (RRID:SCR_002165) Copy   

•   Source: SciCrunch Registry

http://www.ecoli-york.org/

A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium.

Proper citation: EchoBASE (RRID:SCR_002430) Copy   

•   Source: SciCrunch Registry

http://www.tanpaku.org/autophagy/

Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes.

Proper citation: Autophagy Database (RRID:SCR_002671) Copy   

•   Source: SciCrunch Registry

http://domine.utdallas.edu

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014)

Proper citation: DOMINE: Database of Protein Interactions (RRID:SCR_002399) Copy   

•   Source: SciCrunch Registry

http://ndbserver.rutgers.edu/

A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF).

Proper citation: Nucleic Acid Database (RRID:SCR_003255) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/RefSeq/

Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.

Proper citation: RefSeq (RRID:SCR_003496) Copy   

•   Source: SciCrunch Registry

http://mutdb.org/

Database with annotations for human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene.

Proper citation: MutDB (RRID:SCR_003251) Copy   

•   Source: SciCrunch Registry

http://compbio.uthsc.edu/miRSNP/

Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions.

Proper citation: PolymiRTS (RRID:SCR_003389) Copy   

•   Source: SciCrunch Registry

http://www.phi-base.org/

Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).

Proper citation: PHI-base (RRID:SCR_003331) Copy   

•   Source: SciCrunch Registry

http://mistdb.com

Database which contains the signal transduction proteins for complete and draft bacterial and archaeal genomes. The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes.

Proper citation: MiST - Microbial Signal Transduction database (RRID:SCR_003166) Copy   

•   Source: SciCrunch Registry