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A resource for information pertaining to methodologies, tools and technologies of gene expression. The website offers resources for sequence analysis, database services, and other technologies of gene expression and regulation.
Proper citation: IFTI-Mirage (RRID:SCR_000505) Copy
http://www.cbs.dtu.dk/services/SignalP/
Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
Proper citation: SignalP (RRID:SCR_015644) Copy
http://dynamine.ibsquare.be/submission/
An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DynaMine (RRID:SCR_014559) Copy
http://www.glycosciences.de/tools/linucs/
Service that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. Input: A structure using the extended, non-graphic nomenclature (in ASCII writing) to describe complex carbohydrates as recommended by IUPAC. Output: A linear, unique notation. The source code (written in C), will be distributed so that software developers can easily implement their algorithm within their own application. LINUCS was chosen to fulfill to following conditions: * Input of extended, non-graphic nomenclature to describe carbohydrate structures. * Resulting linear code is closely related to notations and abbreviations recommended by IUPAC. * Number of additional rules to define the priority of the branches is low * Extended nomenclature of complex carbohydrates contains all information to define the hierarchy. * LINUCS is applicable to all types of carbohydrates (macrocyclic system are currently not implemented) . * Remaining unassigned linkage information are tolerated
Proper citation: LINUCS (RRID:SCR_001571) Copy
A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.
Proper citation: cpnDB: A Chaperonin Database (RRID:SCR_002263) Copy
http://ww2.sanbi.ac.za/Dbases.html
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index
Proper citation: Sequence Tag Alignment and Consensus Knowledgebase Database (RRID:SCR_002156) Copy
The Hepatitis C Virus (HCV) Database Project strives to present HCV-associated genetic and immunologic data in a user-friendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.
Proper citation: HCV Databases (RRID:SCR_002863) Copy
Issue
Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.
Proper citation: SPM (RRID:SCR_007037) Copy
Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome.
Proper citation: SoyBase (RRID:SCR_005096) Copy
https://github.com/cmayer/BaitFisher-package
Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.
Proper citation: Baitfisher (RRID:SCR_015985) Copy
http://www.sanger.ac.uk/science/tools/seqtools
Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments.
Proper citation: Belvu (RRID:SCR_015989) Copy
Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences.
Proper citation: Fastml (RRID:SCR_016092) Copy
Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).
Proper citation: Aevol (RRID:SCR_015966) Copy
https://bioinf.eva.mpg.de/anfo/
Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.
Proper citation: Anfo (RRID:SCR_015972) Copy
http://disulfind.dsi.unifi.it/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.
Proper citation: DISULFIND (RRID:SCR_016072) Copy
http://www.sanger.ac.uk/science/tools/seqtools
Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences.
Proper citation: Dotter (RRID:SCR_016080) Copy
https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Exonerate (RRID:SCR_016088) Copy
https://github.com/osallou/cassiopee-c
Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.
Proper citation: Cassiopee (RRID:SCR_016056) Copy
http://cdbfasta.sourceforge.net/
Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records.
Proper citation: Cdbfasta (RRID:SCR_016057) Copy
http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.
Proper citation: Clonalframe (RRID:SCR_016060) Copy
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