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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
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
http://www.cbs.dtu.dk/services/ProP/
Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.
Proper citation: ProP Server (RRID:SCR_014936) Copy
http://mummer.sourceforge.net/
Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.
Proper citation: MUMmer (RRID:SCR_018171) Copy
http://prodata.swmed.edu/promals3d/promals3d.php
Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints.
Proper citation: PROMALS3D (RRID:SCR_018161) Copy
https://github.com/r3fang/SnapTools
Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets.
Proper citation: SnapTools (RRID:SCR_018097) Copy
https://www.ebi.ac.uk/covid-19
EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.
Proper citation: EMBL-EBI COVID-19 Portal (RRID:SCR_018337) Copy
https://bigd.big.ac.cn/ncov/?lang=en
Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data.
Proper citation: 2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) Copy
Software tool for efficiently solving large scale sequence matching tasks.
Proper citation: Vmatch (RRID:SCR_018968) Copy
http://hihg.med.miami.edu/software-download/seqem-version-1.0
Online tool for utilizing a genotype calling algorithm for next-generation sequence data.
Proper citation: SeqEM (RRID:SCR_002021) Copy
http://code.google.com/p/rnao/
An ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.
Proper citation: RNA Ontology (RRID:SCR_003470) Copy
http://purl.obolibrary.org/obo/flu/
An application ontology established by a collaborative group of influenza researchers that includes consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)
Proper citation: Influenza Ontology (RRID:SCR_003346) Copy
http://blocks.fhcrc.org/blocks/codehop.html
This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Proper citation: COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) Copy
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
https://www.github.com/arq5x/poretools
Software toolkit for analyzing nanopore sequence data.
Proper citation: Poretools (RRID:SCR_015879) Copy
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
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
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
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
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
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