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https://www.ebi.ac.uk/Tools/psa/emboss_matcher/

Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools.

Proper citation: EMBOSSMatcher (RRID:SCR_017252) Copy   

•   Source: SciCrunch Registry

https://github.com/JosephCrispell/homoplasyFinder/wiki

Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R.

Proper citation: HomoplasyFinder (RRID:SCR_017300) Copy   

•   Source: SciCrunch Registry

https://www.beast2.org/

Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.

Proper citation: BEAST2 (RRID:SCR_017307) Copy   

•   Source: SciCrunch Registry

https://github.com/ISUgenomics/SequelQC

Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data.

Proper citation: SequelQC (RRID:SCR_017279) Copy   

•   Source: SciCrunch Registry

http://mordred.bioc.cam.ac.uk/~rapper/rampage.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure.

Proper citation: RAMPAGE (RRID:SCR_017590) Copy   

•   Source: SciCrunch Registry

https://amoebadb.org/amoeba/

Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers.

Proper citation: AmoebaDB (RRID:SCR_017592) Copy   

•   Source: SciCrunch Registry

http://manaslu.fiserlab.org/MMM/

Web server for modeling protein structure by using Multiple Mapping Method. Approach to sequence-to-structure alignment in comparative protein structure modeling.

Proper citation: Multiple Mapping Method Server (RRID:SCR_018015) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://imputationserver.sph.umich.edu/

Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping.

Proper citation: Michigan Imputation Server (RRID:SCR_017579) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.glycosciences.de/tools/GlycoFragments/

Service that calculates and displays the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MS-spectra. The extended ASCII nomenclature as recommended by IUPAC is used to input the sequence of complex oligosaccharides. However, some additional input rules have to be fulfilled. In case only the topology and composition of the oligosaccharide is known, a simpler way to input carbohydrate sequences is possible. Since the hydroxyl groups of synthetic carbohydrates are often the are protected they have included a way to indicate if sugar residue are persubstituted. Please have a look at the examples of valid input structures.

Proper citation: GlycoFragment (RRID:SCR_001573) Copy   

•   Source: SciCrunch Registry

http://www.transcriptionfactor.org/index.cgi?Home

Database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of the transcription factor predictions show they are accurate and have wide coverage on a genomic scale. The DBD consists of predicted transcription factor repertoires for 930 completely sequenced genomes.

Proper citation: DBD: Transcription factor prediction database (RRID:SCR_002300) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/services/DictyOGlyc-1.1/

Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.

Proper citation: DictyOGlyc (RRID:SCR_001600) Copy   

•   Source: SciCrunch Registry

http://mirna.imbb.forth.gr/SSCprofiler.html

Tool which can be used to identify novel miRNA gene candidates in the human genome.

Proper citation: SSCprofiler (RRID:SCR_001282) Copy   

•   Source: SciCrunch Registry

http://www-personal.umich.edu/~jianghui/rseq/

A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.

Proper citation: rSeq (RRID:SCR_000562) Copy   

•   Source: SciCrunch Registry

http://sonorus.princeton.edu/hefalmp/

HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool.

Proper citation: Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) Copy   

•   Source: SciCrunch Registry

http://www.proweb.org/coddle/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene.

Proper citation: Coddle-Codons Optimized to Discover Deleterious LEsions (RRID:SCR_003003) Copy   

•   Source: SciCrunch Registry