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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BAliBASE Resource Report Resource Website 10+ mentions |
BAliBASE (RRID:SCR_001940) | BAliBASE | data or information resource, data set, software resource, source code |
A collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. Within the resource, users can look at a list of all the alignments, download the whole database by ftp, get the "c" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets. |
benchmark alignment, circular permutation, transmembrane sequence, multiple sequence alignment, benchmark, reference alignment, sequence alignment, sequence, alignment |
is listed by: OMICtools has parent organization: University of Strasbourg; Strasbourg; France |
PMID:16044462 PMID:11125126 PMID:10068696 |
Free, Available for download, Freely available | nif-0000-02594, OMICS_00971 | http://www-bio3d-igbmc.u-strasbg.fr/balibase/, http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html | SCR_001940 | Benchmark Alignment dataBASE | 2026-08-29 11:28:29 | 28 | |||||
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International Gene Trap Consortium Resource Report Resource Website 10+ mentions |
International Gene Trap Consortium (RRID:SCR_002305) | IGTC | biomaterial supply resource, cell repository, material resource | Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy). | embryo, embryonic, gene, genome, allele, analysis, assay, bioinformatics, blastocyst, cell, colony, consortium, genotyping, hybridization, in situ, international, knockout, murine, mutant, mutation, probe, qpcr, researcher, scientist, sequence, stem cell, tagging, trap, vector, cell line, embryonic stem cell line, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is related to: Centre for Modeling Human Disease Gene Trap Resource has parent organization: University of California at San Francisco; California; USA is parent organization of: International Gene Trap Consortium Pathways |
NCRR P41 RR01081 | PMID:16381950 | Restricted | nif-0000-00036 | https://igtc.org/ | SCR_002305 | International Gene Trap Consortium | 2026-08-29 11:28:39 | 43 | ||||
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WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation Resource Report Resource Website 10+ mentions |
WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation (RRID:SCR_005321) | WebApollo | production service resource, service resource, software resource, source code | WebApollo is an extensible web-based sequence annotation editor for community annotation. No software download is required and the annotations are saved to a centralized database with real-time annotation updating. (The edit server mediates annotation changes made by multiple users.) The Web based client uses JBrowse, is fast and highly interactive. WebApollo accesses many types of genomic data including access to public data from UCSC, Ensembl, and GMOD Chado databases. Source code (BSD License) * Client source code: https://github.com/berkeleybop/jbrowse * Annotation editing engine: http://code.google.com/p/apollo-web * Data model and I/O layer: http://code.google.com/p/gbol * Trellis server code: http://code.google.com/p/genomancer | sequence, annotation, genome |
has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Georgetown University; Washington D.C.; USA |
nlx_144381 | SCR_005321 | WebApollo - A Web-Based Sequence Annotation Editor for Community Annotation | 2026-08-29 11:28:42 | 13 | ||||||||
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COILS: Prediction of Coiled Coil Regions in Proteins Resource Report Resource Website 100+ mentions |
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) | data processing software, software application, software resource | COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. | software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1126/science.252.5009.1162 | biotools:ncoils, OMICS_07850, nif-0000-30263 | https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ | https://sources.debian.org/src/ncoils/ | SCR_008440 | COILS Server | 2026-08-29 11:28:48 | 169 | ||||||
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Trim Galore Resource Report Resource Website 5000+ mentions Rating or validation data |
Trim Galore (RRID:SCR_011847) | Trim Galore! | data processing software, software application, software resource | Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data. | Automate, quality, adapter, trimming, remove, biased, methylation, position, RRBS, reduced, representation, bisulfite, data, sequence, wrapper, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute works with: cutadapt |
Free, Available for download, Freely available | biotools:trim_galore, OMICS_01096, SCR_016946 | https://github.com/FelixKrueger/TrimGalore, https://bio.tools/trim_galore, https://sources.debian.org/src/trim-galore/ | SCR_011847 | TrimGalore | 2026-08-29 11:28:41 | 7582 | ||||||
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AfterQC Resource Report Resource Website 10+ mentions |
AfterQC (RRID:SCR_016390) | data processing software, software application, software resource | Software that performs automatic filtering, trimming, error removing, and quality control for fastq data. | fastq, qc, editing, filtering, trimming, dna, rna, seq, sequence, sequencing, poly, pair-end, python | PMID:28361673 | Free, Available for download | SCR_016390 | After QC | 2026-08-29 11:28:50 | 15 | |||||||||
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Albacore Resource Report Resource Website 100+ mentions |
Albacore (RRID:SCR_015897) | data processing software, software application, software resource | Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data. | sequence, dna, raw data, event detection, single-read, nanopore, basecaller, basecaller software, dockerfile | Free, Available for download | SCR_015897 | 2026-08-29 11:28:50 | 437 | |||||||||||
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Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | data processing software, software application, software resource | Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies. | Assembly, de novo, long, uncorrected, read, raw, contig, consensus, step, data, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
A*STAR ; Singapore ; Croatian Academy of Sciences and Arts ; Croatian Science Foundation |
DOI:10.1101/068122 | Free, Available for download, Freely available | OMICS_25714, biotools:Racon, BioTools:Racon | https://bio.tools/Racon, https://sources.debian.org/src/racon/ | SCR_017642 | 2026-08-29 11:28:53 | 177 | ||||||
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TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | data processing software, software application, software resource, standalone software | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder, https://sources.debian.org/src/transdecoder/, https://github.com/TransDecoder/TransDecoder/wiki | SCR_017647 | , Find Coding Regions Within Transcripts | 2026-08-29 11:28:48 | 1572 | |||||||
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Recognition of Errors in Assemblies using Paired Reads Resource Report Resource Website 1+ mentions |
Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) | REAPR | data processing software, software application, software resource | Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls. | Identify, error, genome, assembly, without, reference, sequence, incorrect, scaffold, error |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
European Union ; JSPS KAKENHI ; Wellcome Trust |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-08-29 11:28:53 | 2 | |||||
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ExonerateTransferAnnotation Resource Report Resource Website |
ExonerateTransferAnnotation (RRID:SCR_017557) | data processing software, software application, software resource | Software tool as pipeline to make anntotations using cDNA and CDS sequences. | Exonerate, transfer, annotation, cDNA, CDS, sequence, pipeline, gene | uses: Exonerate | Free, Available for download, Freely available | SCR_017557 | Resource | 2026-08-29 11:28:53 | 0 | |||||||||
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Augur Resource Report Resource Website 50+ mentions |
Augur (RRID:SCR_023964) | software resource, software toolkit | Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines. | track evolution, sequence, serological data. | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/augur/, https://docs.nextstrain.org/projects/augur/en/stable/ | SCR_023964 | augur | 2026-08-29 11:29:00 | 88 | ||||||||
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Marvel Resource Report Resource Website 1+ mentions |
Marvel (RRID:SCR_017621) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software set of tools that facilitate overlapping, patching, correction and assembly of noisy long reads. | Overlapping, patching, correction, assembly, noisy, long, read, sequence, align | Free, Available for download, Freely available | SCR_017621 | 2026-08-29 11:28:11 | 2 | |||||||||||
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OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, data processing software, software application, software resource | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder | SCR_017118 | OrthoFinder2, OrthoFinder | 2026-08-29 11:28:10 | 3413 | |||||
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PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | analysis service resource, data access protocol, data or information resource, database, production service resource, service resource, software resource, web service | Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. | analysis, pairwise, identity, distribution, viral, family, sequence, classification, data, taxonomy | has parent organization: NCBI | National Library of Medicine | PMID:25119676 | Free, Public | SCR_016642 | PAirwise Sequence Comparison | 2026-08-29 11:27:42 | 6 | ||||||
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IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | alignment software, analysis service resource, data or information resource, data processing software, image analysis software, portal, production service resource, service resource, software application, software resource | Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. | Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian |
CNRS ; GENCI ; MESR ; NHMRC ; Université Montpellier 2 ; France |
PMID:22647994 PMID:23995877 PMID:22665256 |
Restricted | biotools:IMGt_HighV-QUESt | https://bio.tools/IMGT_HighV-QUEST | SCR_018196 | IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal | 2026-08-29 11:27:46 | 15 | |||||
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SignalP Resource Report Resource Website 10000+ mentions |
SignalP (RRID:SCR_015644) | software resource, web application | Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | prediction, signal peptide, cleavage site, amino acid, sequence, artificial neural network |
is listed by: SoftCite has parent organization: DTU Center for Biological Sequence Analysis |
PMID:28451972 | Freely available, Acknowledgment requested, Free, Available for download, Runs on Windows, Runs on Mac OS | SCR_015644 | 2026-08-29 11:28:14 | 10033 | |||||||||
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DynaMine Resource Report Resource Website 10+ mentions |
DynaMine (RRID:SCR_014559) | software resource, web application | An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | nmr, protein folding, prediction, fasta, sequence, dynamics | PMID:24225580 | THIS RESOURCE IS NO LONGER IN SERVICE | http://dynamine.ibsquare.be | SCR_014559 | 2026-08-29 11:28:22 | 44 | |||||||||
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Xenopus Gene Collection Resource Report Resource Website 1+ mentions |
Xenopus Gene Collection (RRID:SCR_007023) | XGC | biomaterial supply resource, material resource | NIH initiative to support production of cDNA libraries, clones and 5'/3' sequences and to provide set of full-length (open reading frame) sequences and cDNA clones of expressed genes for Xenopus laevis and Xenopus tropicalis. Clones distribution is outsourced to for profit companies. Project concluded in September 2008. Resources generated by XGC are publicly accessible to biomedical research community. All sequences are deposited into GenBank.Corresponding clones are available through IMAGE clone distribution network. With conclusion of XGC project, GenBank records of XGC sequences will be frozen, without further updates. Since knowledge of what constitutes full-length coding region for some of genes and transcripts for which we have XGC clones will likely change in future, users planning to order XGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | est sequencing, expressed gene, frog, gene, adult, cdna, genomic, open reading frame, sequencing, stage, tag, xenopus laevis, xenopus tropicalis, sequence, expressed sequence tag, cdna, vector, cdna library, clone, 5'/3' sequence, frozen |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: ATCC is related to: GenBank is related to: Invitrogen Clones has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research ; NIH |
Free, Freely available | nif-0000-00224 | https://genecollections.nci.nih.gov/XGC/ | SCR_007023 | Xenopus Gene Collection | 2026-08-29 11:30:48 | 4 | |||||
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Zebrafish Gene Collection Resource Report Resource Website 1+ mentions |
Zebrafish Gene Collection (RRID:SCR_007054) | ZGC | biomaterial supply resource, material resource | Part of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cdna library, clone, sequence, full-length open reading frame, cdna clone, frozen, fish, gene, genetic, genome, genomic |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: Mammalian Gene Collection is related to: GenBank is related to: ATCC has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | nif-0000-00567 | https://genecollections.nci.nih.gov/ZGC/ | SCR_007054 | Zebrafish Gene Collection | 2026-08-29 11:30:59 | 1 |
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