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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
NAT/NCS2 Hound
 
Resource Report
Resource Website
1+ mentions
NAT/NCS2 Hound (RRID:SCR_016473) NAT, NCS2 web application, software resource, data processing software, sequence analysis software, software application, data analysis software Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins. protein, sequence, scan, identify, evolutionary, classify, prokaryotic, nucleobase, transporter, protein, amino acid, conserved is listed by: OMICtools
has parent organization: University of Thessaly; Thessaly; Greece
DOI:10.1101/332452 Free, Available to download, Freely available SCR_016473 Nucleobase Ascorbate Transporter, NCS2:Nucleobase Cation Symporter 2 2026-08-02 09:07:24 1
1000 Fungal Genome Project
 
Resource Report
Resource Website
1+ mentions
1000 Fungal Genome Project (RRID:SCR_016463) organism-related portal, web service, software resource, data access protocol, project portal, data or information resource, topical portal, database, portal Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment. project, genomic, information, fungi, data, sequence, energy, environment is related to: MycoCosm
is related to: Lawrence Berkeley National Laboratory
has parent organization: DOE Joint Genome Institute
the DOE Office of Biological and Environmental Research (BER) Free, Register for an account SCR_016463 2026-08-02 09:07:18 2
MentaLiST
 
Resource Report
Resource Website
1+ mentions
MentaLiST (RRID:SCR_016469) software resource, data processing software, sequence analysis software, software application, data analysis software Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools is listed by: bio.tools
is listed by: Debian
Canadian Institute for Health Research ;
Genome Canada ;
Genome BC
PMID:29319471 Free, Available for download, Freely available biotools:mentalist https://bio.tools/mentalist SCR_016469 2026-08-02 09:07:21 8
Centrifuge Classifier
 
Resource Report
Resource Website
1+ mentions
Centrifuge Classifier (RRID:SCR_016665) software resource, data processing software, sequence analysis software, software application, data analysis software Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: OMICtools
is related to: Pavian
has parent organization: Center for Computational Biology at JHU
U. S. Army Research Office W911NF1410490;
NSF ABI1356078;
NHGRI R01 HG006677;
NIGMS R01 GM083873
DOI:10.1101/gr.210641.116 Free, Available for download, Freely available biotools:centrifuge, OMICS_12217 https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ SCR_016665 2026-08-02 09:07:21 9
PaVE
 
Resource Report
Resource Website
100+ mentions
PaVE (RRID:SCR_016599) PaVE web application, software resource, production service resource, data or information resource, database, service resource, data analysis service, analysis service resource Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information. data, curated, papilloma, virus, genomic, sequence, analysis, storage, annotation, FASEB list is listed by: NIAID NIAID ZIA AI001071 PMID:28053164 Open source SCR_016599 PapillomaVirus Episteme, Papillomavirus Episteme 2026-08-02 09:07:20 125
BLASTClust
 
Resource Report
Resource Website
50+ mentions
BLASTClust (RRID:SCR_016641) software resource, data processing software, sequence analysis software, software application, data analysis software Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets. cluster, protein, nucleotide, sequence, pairwise, match, sequence is listed by: SoftCite
has parent organization: NCBI
works with: NCBI BLAST
Free, Freely available SCR_016641 2026-08-02 09:07:27 88
Genotyping
 
Resource Report
Resource Website
10+ mentions
Genotyping (RRID:SCR_016645) web service, software resource, data access protocol, data processing software, sequence analysis software, software application, data analysis software Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus. identify, genotype, viral, sequence, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: NCBI
works with: NCBI BLAST
Free, Freely available biotools:ncbi_genotyping https://bio.tools/ncbi_genotyping SCR_016645 2026-08-02 09:07:27 31
Open Reading Frame Finder
 
Resource Report
Resource Website
1000+ mentions
Open Reading Frame Finder (RRID:SCR_016643) ORF finder software resource, production service resource, data processing software, sequence analysis software, service resource, software application, data analysis software, analysis service resource Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long. search, open, reading, frame, DNA, sequence, ORF, protein, translation, data, encoding, segment, verify uses: BLASTP
has parent organization: NCBI
Free, Available for download, Freely available SCR_016643 Open Reading Frame finder, Open Reading Frame Finder 2026-08-02 09:07:21 1428
Libra
 
Resource Report
Resource Website
Libra (RRID:SCR_016608) software resource, data processing software, sequence analysis software, data analytics software, data analysis software, software application Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools is listed by: bio.tools
is listed by: Debian
NSF 1640775 Free, Available for download, Freely available biotools:Libra_k-mer https://bio.tools/Libra_k-mer SCR_016608 2026-08-02 09:07:26 0
dCAS
 
Resource Report
Resource Website
dCAS (RRID:SCR_016612) dCAS web application, software resource Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. automate, large, scale, cDNA, sequence, analysis, BLAST, database, gene is listed by: NIAID THIS RESOURCE IS NO LONGER IN SERVICE SCR_016612 Desktop cDNA Annotation System 2026-08-02 09:07:20 0
CCTOP
 
Resource Report
Resource Website
10+ mentions
CCTOP (RRID:SCR_016963) CCTOP web service, software resource, production service resource, data access protocol, service resource, analysis service resource Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them. transmembrane, topology, prediction, signal, peptide, globular, protein, discrimination, amino, acid, sequence, region, orientation, segment, bio.tools is listed by: Debian
is listed by: bio.tools
works with: PDBTM
works with: Topology Data Bank of Transmembrane Proteins
works with: TopDom
Hungarian Scientific Research Fund PMID:25943549 Free, Freely available biotools:cctop https://bio.tools/cctop SCR_016963 CCTOP, Consensus Constrained TOPology 2026-08-02 09:07:31 29
ALGGEN-PROMO
 
Resource Report
Resource Website
100+ mentions
ALGGEN-PROMO (RRID:SCR_016926) organization portal, software resource, data or information resource, data processing software, sequence analysis software, portal, service resource, software application, data analysis software, laboratory portal Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches. identify, transcription, factor, binding, site, DNA, sequence, species, regulatory, element, search PMID:11847087
PMID:12824386
Free, Available for download, Freely available SCR_016926 PROMO, ALGorithmics and GENetics PROMO, ALGGEN, ALGGEN-PROMO 2026-08-02 09:07:24 354
smMIPfil
 
Resource Report
Resource Website
1+ mentions
smMIPfil (RRID:SCR_016892) data analysis software, software resource, data processing software, software application Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required. nucleotide, DNA, read, unique, molecular, identifier, single, inversion, probe, data, analysis, mutation, sequence requires: SAMTOOLS Free, Available for download, Freely available SCR_016892 single molecule Molecular Inversion Probesfil, smMIPfil 2026-08-02 09:07:30 2
CRISPR-P
 
Resource Report
Resource Website
10+ mentions
CRISPR-P (RRID:SCR_016941) web service, software resource, production service resource, data access protocol, service resource, analysis service resource Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment. synthetic, single, RNA, CRISP, plant, Cas9, target, DNA, sequence, analysis, restriction, enzyme, sgRNA, bio.tools is listed by: Debian
is listed by: bio.tools
National Basic Research Program of China ;
Program for New Century Excellent Talents in University ;
Fundamental Research Funds for the Central Universities
PMID:24719468 Free, Freely available biotools:CRISPR-P https://bio.tools/CRISPR-P SCR_016941 CRISPR-P 2.0, Clustered Regularly Interspaced Short Palindromic Repeats P, CRISPR P 2026-08-02 09:07:31 30
Bestus Bioinformaticus Duk
 
Resource Report
Resource Website
100+ mentions
Bestus Bioinformaticus Duk (RRID:SCR_016969) BBDuk software resource, data processing software, data analytics software, data analysis software, software application Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass. sequencing, data, quality, trimming, filtering, masking, operation, single, tool, adapter, contaminant, sequence, GC, length, entropy, format, conversion, histogram, kmer, estimation, decontamination is listed by: Bestus Bioinformaticus Tools
has parent organization: DOE Joint Genome Institute
works with: Reformat
http://seqanswers.com/forums/showthread.php?t=42776, https://www.geneious.com/plugins/bbduk/#links SCR_016969 BB Duk, Decontamination Using Kmers, Bestus Bioinformaticus Decontamination using kmers, BBDuk2, BBDUK, BBDuk, BBDuk 2, Bestus Bioinformaticus Decontamination Using kmers 2026-08-02 09:07:32 184
PICRUSt
 
Resource Report
Resource Website
10+ mentions
PICRUSt (RRID:SCR_016855) PICRUSt simulation software, software resource, software application Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome. predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA is related to: PICRUSt2 Canadian Institutes of Health Research ;
Canada Research Chairs program ;
Howard Hughes Medical Institute ;
NIDDK P01 DK078669;
NHGRI U01 HG004866;
NHGRI R01 HG004872;
Crohn’s and Colitis Foundation of America ;
Sloan Foundation ;
NHGRI R01 HG005969;
NSF CAREER DBI1053486;
ARO W911NF1110473
PMID:23975157 Free, Available for download, Freely available SCR_016856 SCR_016855 Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt 2026-08-02 09:07:32 36
KAT
 
Resource Report
Resource Website
10+ mentions
KAT (RRID:SCR_016741) KAT software toolkit, software resource, data processing software, software application, data analysis software Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies. generate, analyse, compare, k-mer, spectra, sequence, file, quality, control, NGS, dataset, genome, assembly, bio.tools is listed by: Debian
is listed by: bio.tools
BBSRC DOI:10.1093/bioinformatics/btw663 Free, Available for download, Freely available biotools:kat http://www.earlham.ac.uk/kat-tools, https://bio.tools/kat SCR_016741 K-mer Analysis Toolkit 2026-08-02 09:07:28 19
RNAmmer
 
Resource Report
Resource Website
100+ mentions
RNAmmer (RRID:SCR_017075) web service, software resource, production service resource, data access protocol, data processing software, standalone software, service resource, software application, data analysis software, data analysis service, analysis service resource Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes. predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNA has parent organization: Technical University of Denmark; Lyngby; Denmark EMBIO at the University of Oslo ;
Research Council of Norway ;
Danish Center for Scientific Computing ;
European Union
PMID:17452365 Restricted SCR_017075 2026-08-02 09:07:34 103
MITE-Tracker
 
Resource Report
Resource Website
1+ mentions
MITE-Tracker (RRID:SCR_017030) MITE Tracker software resource, data processing software, sequence analysis software, software application, data analysis software Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences. genomic, sequence, discover, miniature, inverted, repeat, transposable, element, clustering, cdhit uses: NCBI BLAST
is listed by: OMICtools
is related to: Python Programming Language
National Institute of Agricultural Technology ;
National Council for Science and Technology ;
Argentina
DOI:10.1186/s12859-018-2376-y Free, Available for download, Freely available OMICS_32242 SCR_017030 MITE Tracker, Miniature Inverted repeats Transposable Elements Tracker 2026-08-02 09:07:25 3
WTDBG
 
Resource Report
Resource Website
50+ mentions
WTDBG (RRID:SCR_017225) software resource, data processing software, sequence analysis software, alignment software, software application, data analysis software, image analysis software Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time. sequence, assembler, de novo, long, noisy, read, likelihood, estimator, genome is listed by: OMICtools
is listed by: Debian
NSFC ;
NHGRI R01 HG010040
PMID:31819265 Free, Available for download, Freely available OMICS_24025 https://github.com/ruanjue/wtdbg, https://sources.debian.org/src/wtdbg2/ SCR_017225 Wtdbg2, wtdgb, Wtdgb, wtdgb2 2026-08-02 09:07:45 57

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