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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CHANCE Resource Report Resource Website 10+ mentions |
CHANCE (RRID:SCR_005330) | CHANCE | software resource | A standalone software package for ChIP-seq quality control and protocol optimization. | is listed by: OMICtools | OMICS_00429 | SCR_005330 | CHiP-seq ANalytics and Confidence Estimation | 2026-02-14 02:01:06 | 12 | |||||||||
|
NCBO Annotator Resource Report Resource Website 1+ mentions |
NCBO Annotator (RRID:SCR_005329) | NCBO Annotator | web service, production service resource, service resource, data access protocol, software resource | A Web service that annotates textual metadata (e.g. journal abstract) with relevant ontology concepts. NCBO uses this Web service to annotate resources in the NCBO Resource Index. They also provide this Web service as a stand-alone service for users. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Their service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards. | ontology, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: STOP has parent organization: BioPortal has parent organization: National Centers for Biomedical Computing has parent organization: Stanford University; Stanford; California |
NHGRI U54 HG004028 | PMID:19483092 | biotools:bioportal, nlx_144389, OMICS_01172 | https://bio.tools/bioportal | SCR_005329 | Open Biomedical Annotator, NCBO BioPortal Annotator | 2026-02-14 02:00:54 | 6 | |||||
|
Assembly Likelihood Estimator Resource Report Resource Website |
Assembly Likelihood Estimator (RRID:SCR_005326) | ALE | software resource | Software using a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid discovery of errors and comparisons between similar assemblies. | standalone software, c, python |
is listed by: OMICtools has parent organization: DOE Joint Genome Institute has parent organization: Cornell University; New York; USA |
PMID:23303509 | Open-source license | OMICS_04067 | https://github.com/sc932/ALE | SCR_005326 | ALE: Assembly Likelihood Estimator | 2026-02-14 02:01:06 | 0 | |||||
|
CoPub Resource Report Resource Website 1+ mentions |
CoPub (RRID:SCR_005327) | CoPub | data access protocol, software resource, web service, service resource | Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. | microarray, gene, literature, enrich, annotate, network, database, differential expression, bio.tools |
uses: MEDLINE uses: Gene Ontology is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Netherlands Bioinformatics Centre |
Netherlands Bioinformatics Centre | PMID:18442992 | Free, Public, Acknowledgement requested | OMICS_01178, biotools:copub | https://bio.tools/copub | http://services.nbic.nl/cgi-bin/copub/CoPub.pl | SCR_005327 | 2026-02-14 02:00:52 | 5 | ||||
|
FaBox Resource Report Resource Website 100+ mentions |
FaBox (RRID:SCR_005350) | FaBox | software resource | Tools for splitting, joining and otherwise manipulating FASTA format sequence files. The first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison allowing users to combine the description of data (often in excel spreadsheets) with the actual data (often DNA sequences). Also, producing correct input files for a range of programs seems to be problematic for the average user. Hence, some converters in some of the services have been included as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you''ll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs. This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use. Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER. | fasta, dna, protein sequence, dna sequence, protein, sequence, php |
is listed by: OMICtools has parent organization: Aarhus University; Aarhus; Denmark |
Acknowledgement requested | OMICS_01165 | SCR_005350 | FaBox - an online fasta sequence toolbox | 2026-02-14 02:01:06 | 116 | |||||||
|
PeakSeq Resource Report Resource Website 10+ mentions |
PeakSeq (RRID:SCR_005349) | PeakSeq | software resource | A software program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:19122651 | biotools:peakseq, OMICS_00453 | https://bio.tools/peakseq | SCR_005349 | 2026-02-14 02:00:54 | 39 | |||||||
|
Anne O'Tate Resource Report Resource Website 1+ mentions |
Anne O'Tate (RRID:SCR_005340) | Anne O'Tate | service resource | A web based search tool to help you gain an overview of the set of articles (up to 25,000 most recent articles) retrieved by a PubMed query. Once you enter a query, you can select different types of summary information to view: Important words, Topics, Authors, Affiliations, Journals, Year, Clustered by topic. | database |
is listed by: OMICtools is related to: PubMed has parent organization: University of Illinois at Chicago; Illinois; USA |
PMID:18279519 | OMICS_01171 | SCR_005340 | 2026-02-14 02:01:05 | 1 | ||||||||
|
GEM Resource Report Resource Website 10+ mentions |
GEM (RRID:SCR_005339) | GEM | software resource | Java software for studying protein-DNA interaction using ChIP-seq / ChIP-exo data. It links binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence, resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution. GEM reciprocally improves motif discovery using binding event locations, and binding event predictions using discovered motifs. | chip-seq, chip-exo, genome, event, motif, protein-dna interaction, java, transcription factor, genome sequence, motif discovery, binding event calling |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
PMID:22912568 | OMICS_00441 | SCR_005339 | Genome wide Event finding and Motif discovery, GEM: ChIP-Seq and ChIP-exo analysis tool | 2026-02-14 02:00:52 | 12 | |||||||
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Hiclib Resource Report Resource Website 10+ mentions |
Hiclib (RRID:SCR_005535) | Hiclib | software resource | An Software resource | is listed by: OMICtools | OMICS_00521 | SCR_005535 | 2026-02-14 02:01:08 | 21 | ||||||||||
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SHRiMP Resource Report Resource Website 100+ mentions |
SHRiMP (RRID:SCR_005496) | SHRiMP | software resource | A software package for aligning genomic reads against a target genome. | next generation sequencing, alignment |
is used by: Jambalaya is listed by: OMICtools is related to: Jambalaya is related to: Proovread has parent organization: University of Toronto; Ontario; Canada |
PMID:21278192 | OMICS_00685 | SCR_005496 | SHRiMP - SHort Read Mapping Package | 2026-02-14 02:00:54 | 207 | |||||||
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PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | data repository, storage service resource, data or information resource, service resource, software resource, database | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | 2026-02-14 02:01:06 | 32 | ||||||
|
SMALT Resource Report Resource Website 500+ mentions |
SMALT (RRID:SCR_005498) | SMALT | software resource | Software that aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads. |
is listed by: OMICtools is related to: Sequence Search and Alignment by Hashing Algorithm has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00686 | SCR_005498 | 2026-02-14 02:00:56 | 507 | ||||||||||
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TIGRFAMS Resource Report Resource Website 100+ mentions |
TIGRFAMS (RRID:SCR_005493) | JCVI TIGRFAMS, TIGRFAM | data set, data or information resource, database | Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site. | sequence alignment, hidden markov model, protein sequence, classification, protein, protein family, sequence homology, sequence, homology, function, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: InterPro is related to: InterPro has parent organization: J. Craig Venter Institute |
PMID:23197656 | Free | nif-0000-03560, OMICS_01700, biotools:tigrfams | https://bio.tools/tigrfams | http://www.tigr.org/TIGRFAMs | SCR_005493 | TIGRFAMs | 2026-02-14 02:01:06 | 135 | ||||
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Segemehl Resource Report Resource Website 10+ mentions |
Segemehl (RRID:SCR_005494) | Segemehl | software resource | A software to map short sequencer reads to reference genomes. It is able to detect not only mismatches but also insertions and deletions. Furthermore, it is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Leipzig; Saxony; Germany |
PMID:24512684 PMID:22581174 PMID:19750212 DOI:10.1371/journal.pcbi.1000502 |
Acknowledgement requested, Free, Public | biotools:segemehl, OMICS_00683 | https://bio.tools/segemehl https://sources.debian.org/src/segemehl/ |
SCR_005494 | segemehl - short read mapping with gaps | 2026-02-14 02:00:56 | 45 | |||||
|
PASS Resource Report Resource Website 1000+ mentions |
PASS (RRID:SCR_005490) | PASS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: PASS-bis has parent organization: University of Padua; Padua; Italy |
PMID:19218350 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pass, OMICS_00673 | https://bio.tools/pass | SCR_005490 | PASS: a program to align short sequences | 2026-02-14 02:01:08 | 2085 | |||||
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pyDNase Resource Report Resource Website 10+ mentions |
pyDNase (RRID:SCR_005406) | pyDNase | software resource | A software library for analyzing DNase-seq data. | is listed by: OMICtools | OMICS_00518 | SCR_005406 | 2026-02-14 02:01:07 | 41 | ||||||||||
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NeuroLex Resource Report Resource Website 10+ mentions |
NeuroLex (RRID:SCR_005402) | NeuroLex | narrative resource, data or information resource, wiki | A freely editable semantic wiki for community-based curation of the terms used in Neuroscience. Entries are curated and eventually incorporated into the formal NIFSTD ontology. NeuroLex also includes a Resource branch for community members to freely add neuroscience relevant resources that do not become part of NIFSTD ontology but rather make up the NIF Registry. As part of the NIF, we provide a simple search interface to many different sources of neuroscience information and data. To make this search more effective, we are constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g., neuron is a cell. These categories provide the means to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that we use to describe our data, e.g., anatomical terms, techniques, organism names. Because wikis provide an easy interface for communities to contribute their knowledge, we started the NeuroLex. | behavioral activity, behavioral paradigm, brain region, cell, neuron, disease, molecule, nervous system function, subcellular part, resource type, quality, brain, neuroscience, biological process, cellular anatomy, anatomy, subcellular, subcellular anatomy, organism, neurological disorder, neurologic disease, dysfunction, atlas application, knowledge environment, php, web service, rdf, knowledge management, neuroanatomy, ontology, semantics, lexicon |
is used by: MicroDraw is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Program on Ontologies of Neural Structures is related to: NIFSTD is related to: neuroelectro is related to: Whole Brain Catalog is related to: Linked Neuron Data is related to: SciCrunch Registry is related to: InterLex has parent organization: Neuroscience Information Framework has parent organization: International Neuroinformatics Coordinating Facility is parent organization of: Integrated is parent organization of: Common Upper Mammalian Brain Ontology is parent organization of: SciCrunch Registry |
Neuroscience Information Framework | PMID:24009581 | Creative Commons Attribution License, v3 Unported | OMICS_01703, nlx_144511 | http://www.nitrc.org/projects/incf_neurolex-w | SCR_005402 | NeuroLex.org | 2026-02-14 02:00:55 | 17 | ||||
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Fulcrum Resource Report Resource Website 1+ mentions |
Fulcrum (RRID:SCR_005523) | Fulcrum | software resource | Software to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory. | illumina, 454, read, paired-end read, single-end read, high-throughput sequencing, redundant read, genome, transcriptome, ultra high throughput sequencing |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22419786 | BSD-like license | OMICS_01049 | http://pringlelab.stanford.edu/protocols.html | SCR_005523 | Fulcrum Read Collapser | 2026-02-14 02:01:08 | 4 | |||||
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Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | biotools:maq, OMICS_00668 | https://bio.tools/maq https://sources.debian.org/src/maq/ |
SCR_005485 | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2026-02-14 02:00:56 | 69 | |||||
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MOSAIK Resource Report Resource Website 50+ mentions |
MOSAIK (RRID:SCR_005486) | MOSAIK | software resource | A reference-guided assembler comprising of two main modular programs: MosaikBuild and MosaikAligner. MosaikBuild converts various sequence formats into Mosaik?s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences and produces BAMs as outputs. At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BAM format. Unlike many current read aligners, MOSAIK produces gapped alignments using the Smith-Waterman algorithm. MOSAIK is written in highly portable C++ and currently targetted for the following platforms: Microsoft Windows, Apple Mac OS X, FreeBSD, and Linux operating systems. Other platforms can easily be supported upon request. MOSAIK is multithreaded. If you have a machine with 8 processors, you can use all 8 processors to align reads faster while using the same memory footprint as when using one processor. MOSAIK supports multiple sequencing technologies. In addition to legacy technologies such as Sanger capillary sequencing, our program supports next generation technologies such as Roche 454, Illumina, AB SOLiD, and experimental support for the Helicos Heliscope. | next-generation sequencing, alignment, smith-waterman algorithm, c++, computational biology, reference guided aligner |
is listed by: OMICtools is listed by: Debian is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: Google Code |
Free, Freely available | OMICS_00669 | https://sources.debian.org/src/mosaik-aligner/ | SCR_005486 | mosaik-aligner | 2026-02-14 02:01:08 | 86 |
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