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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html
Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.
Proper citation: Entrez (RRID:SCR_016640) Copy
https://blast.ncbi.nlm.nih.gov/moleblast/moleblast.cgi
Software tool that helps taxonomists find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results.
Proper citation: MOLE-BLAST (RRID:SCR_016644) Copy
http://ec2-52-91-98-53.compute-1.amazonaws.com/run/
Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data.
Proper citation: Clonotator (RRID:SCR_016730) Copy
https://github.com/TGAC/RAMPART
Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems.
Proper citation: Rampart (RRID:SCR_016742) Copy
https://bioconductor.org/packages/release/bioc/html/Rsubread.html
Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.
Proper citation: Rsubread (RRID:SCR_016945) Copy
https://bioconductor.org/packages/release/bioc/html/Biostrings.html
Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Proper citation: Biostrings (RRID:SCR_016949) Copy
http://prosightlite.northwestern.edu/
Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.
Proper citation: ProSight Lite (RRID:SCR_016908) Copy
http://cab.spbu.ru/software/rnaspades/
Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9.
Proper citation: rnaSPAdes (RRID:SCR_016992) Copy
http://cqb.pku.edu.cn/ZhuLab/PPR_Meta
Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PPR-Meta (RRID:SCR_016915) Copy
http://www.clustal.org/clustal2/
Software tool for nucleotide sequence alignment. Graphical version of multiple sequence alignment program for DNA and proteins. Windows interface for ClustalW multiple sequence alignment program. Provides integrated environment for performing multiple sequence and profile alignments and analyzing results. Available on Linux, Mac and Windows.
Proper citation: Clustal 2 (RRID:SCR_017055) Copy
http://www.cisreg.ca/cgi-bin/NHR-scan/nhr_scan.cgi
Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications.
Proper citation: Nuclear Hormone Receptor Scan (RRID:SCR_016975) 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
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://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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