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http://biobases.ibch.poznan.pl/ncRNA/

It is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota. The primary source of sequences included in the database was the GenBank. Additional annotation information for mouse and human ncRNAs was derived from FANTOM3 database and H-inviational Integrated Database of Annotated Human Genes version 3.4, respectively. Genome mapping information was derived from tha data available at the UCSC Genome Browser site. The sequences and annotations of small cytoplasmic RNAs from bacteria, for which annotation is lacking in the genome sequences, were derived from the Rfam database. The microRNAs or snoRNAs which were available in previous editions, as well as other housekeeping (infrastructural) RNAs (e.g. rRNA, tRNA, snRNA, SRP RNA) are not included in our database to avoid redundancy with more specialized databases which emerged in recent years.

Proper citation: Noncoding RNA database (RRID:SCR_007815) Copy   

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http://www.cmbi.ru.nl/phylopat

A database of phylogenetic patterns of evolution between 46 different species. PhyloPat uses the latest release of EnsMart (release 52), and their one-to-one, one-to-many and many-to-many orthologies. First, we stored all of the Ensembl IDs within the 46 species, and the orthologies between them. Second, we determined the evolutionary order of the studied species using the NCBI Taxonomy database. The phylogenetic tree of these species can be viewed here. Third, we used this phylogenetic tree as a starting point for building our phylogenetic lineages. For each gene in the first species (S. cerevisiae), we looked for orthologs in the other species. All orthologs were added to the phylogenetic lineage, and in the next round were checked for orthologs themselves, until no more orthologies were found for any of the genes. This process was repeated for all genes in all species that were not connected to any phylogenetic lineage yet. The complete phylogenetic lineage determination generated 329,998 phylogenetic lineages, consisting of 973,821 genes. These lineages can be queried here by phylogenetic patterns, MySQL regular expressions or simply a list of Ensembl/EMBL/EntrezGene/HGNC IDs. Output can be given in HTML, Excel or plain text format.

Proper citation: PhyloPat (RRID:SCR_007851) Copy   

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http://phylomedb.bioinfo.cipf.es

Database for phylomes, that is, complete collections of phylogenetic trees for all proteins encoded in a given genome. It aims at providing a repository of high-quality phylogenies and alignments for proteins encoded in model species. To derive a phylome, each protein encoded in a given genome is used as a seed to retrieve its homologs in other complete genomes. These sequences are aligned and processed to derive reliable phylogenies using several phylogenetic methods. Besides providing the evolutionary history of the gene families, phylomeDB includes phylogeny based predictions of orthology and paralogy relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhylomeDB (RRID:SCR_007850) Copy   

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http://www.partigenedb.org/

A publicly available database resource containing the assembled partial genomes for ~700 eukaryotic organisms. Partial genomes are generated from expressed sequence tag datasets containing more than 1000 sequences. PartiGeneDB allows users to view sets of genes and identify genes of interest in organisms for which a full genome is not currently available. PartiGeneDB is automatically updated to include new organism datasets as they are generated. PartiGeneDB provides four portals of entry into the database. It is hosted and supported by the Hospital for Sick Children, Toronto. In addition to providing a comprehensive resource facilitating comparative analyses, PartiGeneDB allows researchers to access the partial genomes of organisms that may not be available elsewhere. However, we recommend and encourage users interested in exploring datasets from a single organism in more depth, that you visit the specific web sites associated with the sequencing effort associated with that organism .

Proper citation: PartiGeneDB (RRID:SCR_007848) Copy   

•   Source: SciCrunch Registry

http://metacyc.org/

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,200 pathways from more than 1,600 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes.

Proper citation: MetaCyc (RRID:SCR_007778) Copy   

•   Source: SciCrunch Registry

http://merops.sanger.ac.uk/

An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.

Proper citation: MEROPS (RRID:SCR_007777) Copy   

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http://locate.imb.uq.edu.au/

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications.

Proper citation: LOCATE: subcellular localization database (RRID:SCR_007763) Copy   

•   Source: SciCrunch Registry

http://www.mgc.ac.cn/VFs/

An integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma). VFDB is a platform for further study of comparative pathogenomics. Major features include tabular comparison of pathogenomic composition in terms of virulence, multiple alignments and statistic analysis of homologous virulence genes, and graphical comparison of pathogenomic organization of VFs. Category: Genomics Databases (non-vertebrate) Subcategory: Prokaryotic genome databases

Proper citation: VFDB - Virulence Factors of Bacterial Pathogens (RRID:SCR_007969) Copy   

•   Source: SciCrunch Registry

http://tdrtargets.org/

This database functions both as a website where researchers can look for information on their targets of interest; and as a tool for prioritization of targets in whole genomes. Using the database as a tool, researchers can quickly prioritize a genome of interest by performing any number of individual queries on a species of interest, then assigning numerical weights to each query (in the history page) to finally obtain a ranked list of genes by combining the weighted queries. This site is part of a WHO/TDR project seeking to exploit the availability of diverse datasets to facilitate the identification and prioritization of drug targets in pathogens causing neglected diseases.

Proper citation: TDR Targets Database (RRID:SCR_007963) Copy   

•   Source: SciCrunch Registry

http://bioafrica.mrc.ac.za/rnavirusdb/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments (in species where more than one isolate has been fully sequenced) and contains translated genome sequences for all species. It has been created for two main purposes: to facilitate the comparative analysis of RNA viruses and to become a hub for other, more specialised virus Web sites.

Proper citation: RNA Virus Database (RRID:SCR_007899) Copy   

•   Source: SciCrunch Registry

http://statgen.ncsu.edu/asg/

Alternative splicing essentially increases the diversity of the transcriptome and has important implications for physiology, development and the genesis of diseases. This resource uses a different approach to investigate alternative splicing (instead of the conventional case-by case fashion) and integrates all transcripts derived from a gene into a single splicing graph. ASG is a database of splicing graphs for human genes, using transcript information from various major sources (Ensembl, RefSeq, STACK, TIGR and UniGene). Each transcript corresponds to a path in the graph, and alternative splicing is displayed by bifurcations. This representation preserves the relationships between different splicing variants and allows us to investigate systematically all possible putative transcripts. Web interface allows users to display the splicing graphs, to interactively assemble transcripts and to access their sequences as well as neighboring genomic regions. ASG also provide for each gene, an exhaustive pre-computed catalog of putative transcriptsin total more than 1.2 million sequences. It has found that ~65 of the investigated genes show evidence for alternative splicing, and in 5 of the cases, a single gene might produce over 100 transcripts.

Proper citation: Alternate splicing gallery (RRID:SCR_008129) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/placnet/

Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools.

Proper citation: Placnet (RRID:SCR_024176) Copy   

•   Source: SciCrunch Registry

https://prinseq.sourceforge.net/

Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format.

Proper citation: PRINSEQ (RRID:SCR_024178) Copy   

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https://sourceforge.net/projects/poamsa/

Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.

Proper citation: POA (RRID:SCR_024172) Copy   

•   Source: SciCrunch Registry

https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index

Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.

Proper citation: PLIP (RRID:SCR_024173) Copy   

•   Source: SciCrunch Registry

https://github.com/Washington-University/CiftiLib

Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files.

Proper citation: CiftiLib (RRID:SCR_023996) Copy   

•   Source: SciCrunch Registry

https://github.com/COMBINE-lab/RapMap

Software tool for mapping RNA-seq reads to transcriptomes. Used for rapid sensitive and accurate read mapping via quasi-mapping

Proper citation: rapmap (RRID:SCR_024204) Copy   

•   Source: SciCrunch Registry

https://github.com/rvaser/bioparser/

Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

Proper citation: Bioparser (RRID:SCR_024065) Copy   

•   Source: SciCrunch Registry

https://github.com/silx-kit/pyFAI

Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments.

Proper citation: pyFAI (RRID:SCR_024186) Copy   

•   Source: SciCrunch Registry

https://github.com/biod/BioD

Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations.

Proper citation: BioD (RRID:SCR_024062) Copy   

•   Source: SciCrunch Registry