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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Genotyping Resource Report Resource Website 10+ mentions |
Genotyping (RRID:SCR_016645) | data access protocol, sequence analysis software, software application, data analysis software, web service, software resource, data processing 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 | 2025-04-08 11:14:43 | 27 | ||||||||
|
Open Reading Frame Finder Resource Report Resource Website 1000+ mentions |
Open Reading Frame Finder (RRID:SCR_016643) | ORF finder | sequence analysis software, software application, data analysis software, production service resource, software resource, service resource, analysis service resource, data processing software | 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 | 2025-04-08 11:14:43 | 1281 | ||||||||
|
Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | sequence analysis software, data analytics software, software application, data analysis software, software resource, data processing software | 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 | 2025-04-08 11:14:43 | 0 | |||||||
|
dCAS Resource Report Resource Website |
dCAS (RRID:SCR_016612) | dCAS | software resource, web application | 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. | automate, large, scale, cDNA, sequence, analysis, BLAST, database, gene | is listed by: NIAID | Free, Available for download, Freely available | SCR_016612 | Desktop cDNA Annotation System | 2025-04-08 11:14:43 | 0 | ||||||||
|
KAT Resource Report Resource Website 10+ mentions |
KAT (RRID:SCR_016741) | KAT | software application, data analysis software, software toolkit, software resource, data processing 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 | 2025-04-08 11:14:45 | 13 | ||||
|
Clone Manager Software Resource Report Resource Website 10+ mentions |
Clone Manager Software (RRID:SCR_014521) | workflow software, software application, simulation software, software resource, data processing software | A software system to assist with cloning simulation, enzyme operations, and graphic map drawing. Clone Manager can also be used as a way to view or edit sequence files, find open reading frames, translate genes, or find genes or text in files. Clone Manager Professional is an upgraded version of Clone Manager Basic. | workflow software, simulation software, enzyme, clone, cloning simulation, graphic map, sequence, view, edit | Price varies based on license type, Professional and Basic versions are available | SCR_014521 | 2025-04-08 11:12:21 | 46 | |||||||||||
|
Unifrac Resource Report Resource Website 500+ mentions |
Unifrac (RRID:SCR_014616) | data analysis software, software resource, software application, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample. | microbiome, comparison, microbial community, phylogenetic tree, sequence | is listed by: Human Microbiome Project | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014616 | 2025-04-08 11:12:25 | 822 | ||||||||||
|
Metapath Resource Report Resource Website 10+ mentions |
Metapath (RRID:SCR_014621) | data analysis software, software resource, software application, data processing software | A statistical package for comparing metagenomic data-sets at the pathway level. It relies on a combination of metagenomic sequence data and prior metabolic pathway knowledge, which is pulled from KEGG. | microbiome, statistics, metagenomics, pathway, sequence, comaprison | is listed by: Human Microbiome Project | Available for download | SCR_014621 | 2025-04-08 11:12:25 | 14 | ||||||||||
|
GapCloser Resource Report Resource Website 500+ mentions |
GapCloser (RRID:SCR_015026) | sequence analysis software, software application, data analysis software, software resource, data processing software, source code | Module of SOAPdenovo2 commonly used independently to close gaps in genome assemblies. | gap closure, genome assembly, sequence | is listed by: SOAP | PMID:23587118 | Free, Available for download | SCR_015026 | 2025-04-08 11:12:41 | 661 | |||||||||
|
CCTOP Resource Report Resource Website 10+ mentions |
CCTOP (RRID:SCR_016963) | CCTOP | data access protocol, production service resource, web service, software resource, 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 | 2025-04-08 11:14:50 | 29 | ||||
|
ALGGEN-PROMO Resource Report Resource Website 100+ mentions |
ALGGEN-PROMO (RRID:SCR_016926) | service resource, organization portal, sequence analysis software, portal, software application, data analysis software, data or information resource, software resource, laboratory portal, data processing software | 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 | 2025-04-08 11:14:49 | 322 | |||||||||
|
smMIPfil Resource Report Resource Website 1+ mentions |
smMIPfil (RRID:SCR_016892) | data analysis software, software resource, software application, data processing software | 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 | 2025-04-08 11:14:48 | 2 | |||||||||
|
CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | data access protocol, production service resource, web service, software resource, 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 | 2025-04-08 11:14:49 | 27 | |||||
|
Bestus Bioinformaticus Duk Resource Report Resource Website 100+ mentions |
Bestus Bioinformaticus Duk (RRID:SCR_016969) | BBDuk | data analytics software, software application, data analysis software, software resource, data processing software | 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 |
Free, Available for download, Freely available | 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 | 2025-04-08 11:14:50 | 150 | |||||||
|
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 | 2025-04-08 11:14:47 | 32 | |||||
|
MITE-Tracker Resource Report Resource Website 1+ mentions |
MITE-Tracker (RRID:SCR_017030) | MITE Tracker | sequence analysis software, software application, data analysis software, software resource, data processing 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 | 2025-04-08 11:14:52 | 2 | |||||
|
matemaker Resource Report Resource Website 1+ mentions |
matemaker (RRID:SCR_017199) | sequence analysis software, standalone software, software application, data analysis software, software resource, data processing software | Software tool to make artificial mate pairs from long sequences for scaffolding. | artificial, mate, pair, long, sequence, scaffolding, genomics, genome, assembly | Free, Available for download, Freely available | SCR_017199 | matemaker v1.0.0 | 2025-04-08 11:14:58 | 3 | ||||||||||
|
RNAmmer Resource Report Resource Website 50+ mentions |
RNAmmer (RRID:SCR_017075) | data access protocol, standalone software, production service resource, data analysis software, software application, web service, software resource, service resource, analysis service resource, data analysis service, data processing software | 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 | 2025-04-08 11:14:53 | 98 | ||||||||
|
WTDBG Resource Report Resource Website 50+ mentions |
WTDBG (RRID:SCR_017225) | image analysis software, sequence analysis software, alignment software, software application, data analysis software, software resource, data processing 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 | 2025-04-08 11:14:59 | 51 | |||||
|
PSMC Resource Report Resource Website 10+ mentions |
PSMC (RRID:SCR_017229) | data analysis software, software resource, software application, data processing software | Software package for implementation of Pairwise Sequentially Markovian Coalescent model. Infers population size history from diploid sequence. | pairwise, sequentially, Markovian, coalescent, model, infer, population, size, history, diploid, sequence | Free, Available for download, Freely available | SCR_017229 | Pairwise Sequentially Markovian Coalescent | 2025-04-08 11:15:00 | 12 |
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