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

Web application for the prediction of transmembrane helices in proteins using Hidden Markov Models. FASTA formatted sequences can be uploaded via file or copy-paste, and output can be formatted as extensive with graphics, extensive without graphics, or one line per protein. Submissions are limited to 10,000 sequences and 4,000,000 amino acids - each sequence is limited to no more than 8,000 amino acids.

Proper citation: TMHMM Server (RRID:SCR_014935) 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.vmatch.de/

Software tool for efficiently solving large scale sequence matching tasks.

Proper citation: Vmatch (RRID:SCR_018968) Copy   

•   Source: SciCrunch Registry

http://www.evocontology.org/site/Main/EvocOntologyDotOrg

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., documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.

Proper citation: eVOC (RRID:SCR_010704) Copy   

•   Source: SciCrunch Registry

https://www.mdc-berlin.de/8551903/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep

Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.

Proper citation: miRDeep (RRID:SCR_010829) Copy   

•   Source: SciCrunch Registry

http://macvector.com

Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions.

Proper citation: MacVector (RRID:SCR_015700) Copy   

•   Source: SciCrunch Registry

https://www.github.com/arq5x/poretools

Software toolkit for analyzing nanopore sequence data.

Proper citation: Poretools (RRID:SCR_015879) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/ariba

Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

Proper citation: Ariba (RRID:SCR_015976) Copy   

•   Source: SciCrunch Registry

http://kmer.sourceforge.net

Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.

Proper citation: Atac (RRID:SCR_015980) Copy   

•   Source: SciCrunch Registry

https://github.com/kdmurray91/axe

Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples.

Proper citation: Axe (RRID:SCR_015984) Copy   

•   Source: SciCrunch Registry

https://github.com/pezmaster31/bamtools/wiki

Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.

Proper citation: Bamtools (RRID:SCR_015987) Copy   

•   Source: SciCrunch Registry

https://github.com/vasilislenis/G-Anchor

Software for comparing large genomes and exploiting highly conserved sequences as evolutionary-stable "anchors". The pipeline maps a newly sequenced genome (assembled in scaffolds) on a reference genome without the need of a supercomputer.

Proper citation: G-Anchor (RRID:SCR_016046) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/seqtools

Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.

Proper citation: Blixem (RRID:SCR_015994) Copy   

•   Source: SciCrunch Registry

http://sing.ei.uvigo.es/ALTER/

Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.

Proper citation: ALTER (RRID:SCR_015968) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/amap-align/

Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method.

Proper citation: AMAP (RRID:SCR_015969) Copy   

•   Source: SciCrunch Registry

http://mbio-serv2.mbioekol.lu.se/ARAGORN/

Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Aragorn (RRID:SCR_015974) Copy   

•   Source: SciCrunch Registry

https://github.com/bbuchfink/diamond

Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.

Proper citation: DIAMOND (RRID:SCR_016071) Copy   

•   Source: SciCrunch Registry

http://sanger-pathogens.github.io/circlator/

Software that automates assembly circularization and produces accurate linear representations of circular sequences. It is used for assembling of DNA sequence data of complete bacterial and small eukaryotic genomes.

Proper citation: Circlator (RRID:SCR_016058) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.hungry.com/clearcut/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Clearcut (RRID:SCR_016059) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/metagenomics/

Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.

Proper citation: MGnify (RRID:SCR_016429) Copy   

•   Source: SciCrunch Registry