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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PRINSEQ Resource Report Resource Website 1000+ mentions |
PRINSEQ (RRID:SCR_005454) | PRINSEQ | service resource, production service resource, analysis service resource, data analysis service | A publicly available tool that is able to filter, reformat and trim your genomic and metagenomic sequence data and provide you summary statistics for your sequence data. The interactive web interface facilitates visualizations of the results and export functionality for subsequent data processing. The standalone lite version is written in Perl and does not require any non-core Perl modules. The lite version is primarily designed for data preprocessing and does not generate summary statistics in graphical form., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, data analysis, genomic sequence data, metagenomic sequence data, summary, perl, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: San Diego State University; California; USA |
PMID:21278185 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01068, biotools:prinseq | http://prinseq.sourceforge.net, https://bio.tools/prinseq | SCR_005454 | PReprocessing and INformation of SEQuences, preprocessing and information of sequences | 2026-07-30 09:27:12 | 1192 | |||||
|
TMA Navigator Resource Report Resource Website 1+ mentions |
TMA Navigator (RRID:SCR_005599) | TMA Navigator | service resource, production service resource, analysis service resource, data analysis service | A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement. | tissue microarray, network, analysis, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23761446 | Acknowledgement requested, Free | biotools:tma_navigator, OMICS_00821 | https://bio.tools/tma_navigator | SCR_005599 | 2026-07-30 09:27:11 | 5 | ||||||
|
ExpressYourself Resource Report Resource Website |
ExpressYourself (RRID:SCR_008881) | ExpressYourself | service resource, production service resource, analysis service resource, data analysis service | A fully integrated platform for processing microarray data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00755, biotools:expressyourself | https://bio.tools/expressyourself | SCR_008881 | ExpressYourself: microarray data processing platform, Express Yourself, Express Yourself: microarray data processing platform | 2026-07-30 09:28:02 | 0 | |||||||
|
waviCGH Resource Report Resource Website 1+ mentions |
waviCGH (RRID:SCR_006662) | waviCGH | service resource, production service resource, analysis service resource, data analysis service | A versatile web-server application for the analysis and visualization of array-CGH data. | genomic, copy number alteration, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20507915 | Acknowledgement requested | OMICS_00739, biotools:wavicgh | https://bio.tools/wavicgh | SCR_006662 | 2026-07-30 09:27:28 | 4 | ||||||
|
Gene Array Analyzer Resource Report Resource Website 1+ mentions |
Gene Array Analyzer (RRID:SCR_008323) | GAA | service resource, production service resource, analysis service resource, data analysis service | Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22123740 | Acknowledgement requested | OMICS_00759, biotools:gene_array_analyzer | https://bio.tools/gene_array_analyzer | SCR_008323 | 2026-07-30 09:27:52 | 5 | ||||||
|
MicroSNiPer Resource Report Resource Website 10+ mentions |
MicroSNiPer (RRID:SCR_009880) | MicroSNiPer | service resource, production service resource, analysis service resource, data analysis service | A web-based application which predicts the impact of a SNP on putative microRNA targets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Mental Health |
PMID:20809528 | biotools:microsniper, OMICS_00388 | https://bio.tools/microsniper | SCR_009880 | 2026-07-30 09:28:25 | 18 | |||||||
|
SVM based method for predicting beta hairpin structures in proteins Resource Report Resource Website 1+ mentions |
SVM based method for predicting beta hairpin structures in proteins (RRID:SCR_008349) | service resource, production service resource, analysis service resource, data analysis service | Bhairpred server is based on machine learning technique SVM using single sequence information, evolutionary profile, predicted and observed secondary structure (as obtained using Psipred and DSSP), predicted and observed accessibility values (as obtainned from Netasa and DSSP). The methods were trained and tested on dataset of 2880 proteins and their performance was evaluated on dataset of 534 proteins used by Thornton (PNAS, 2002). Best prediction results were obtained with hybrid approach that combined prediction results from evolutionary profile, predicted secondary structure and accessibility. | evolutionary, information, protein, protein structure prediction, secondary, sequence, single, svm, technique, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Institute of Microbial Technology; Chandigarh; India |
Institute of Microbial Technology | nif-0000-25213, biotools:bhairpred | https://bio.tools/bhairpred | SCR_008349 | BhairPred | 2026-07-30 09:27:47 | 2 | |||||||
|
GFINDer: Genome Function INtegrated Discoverer Resource Report Resource Website 1+ mentions |
GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) | GFINDer | service resource, production service resource, analysis service resource, data analysis service | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results. | annotation, statistical analysis, mining, genome, function, sequence, functional profile, gene, microarray, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Polytechnic University of Milan; Milan; Italy |
PMID:15980570 PMID:15215397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149256, biotools:gfinder | https://www.hsls.pitt.edu/obrc/index.php?page=URL1098209538, https://bio.tools/gfinder | SCR_008868 | Genome Function INtegrated Discoverer, Genome Function INtegrated Discoverer (GFINDer) | 2026-07-30 09:28:01 | 1 | |||||
|
CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | service resource, production service resource, analysis service resource, data analysis service | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-07-30 09:27:34 | 0 | |||
|
mirTools Resource Report Resource Website 10+ mentions |
mirTools (RRID:SCR_009701) | mirTools | service resource, production service resource, analysis service resource, data analysis service | A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23778453 | OMICS_00365, biotools:mirtools | https://bio.tools/mirtools | SCR_009701 | mirTools 2.0 | 2026-07-30 09:28:23 | 13 | ||||||
|
ESEfinder 3.0 Resource Report Resource Website 100+ mentions |
ESEfinder 3.0 (RRID:SCR_007088) | ESEfinder | service resource, production service resource, analysis service resource, data analysis service | A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements. | exonic splicing enhancer, sr protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
NIGMS GM42699; NCI CA88351; NHGRI HG01696 |
PMID:12824367 | Free for non-profit use, Non-commercial, Acknowledgement requested, Commercial use with license | biotools:esefinder, nif-0000-30496 | http://rulai.cshl.edu/tools/ESE2/, https://bio.tools/esefinder | http://exon.cshl.edu/ESE/ | SCR_007088 | 2026-07-30 09:27:34 | 211 | ||||
|
T-Coffee Resource Report Resource Website 1000+ mentions |
T-Coffee (RRID:SCR_011818) | T-Coffee | service resource, production service resource, analysis service resource, data analysis service | A multiple sequence alignment server which can align Protein, DNA and RNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:10964570 DOI:10.1006/jmbi.2000.4042 |
biotools:tcoffee, OMICS_00989 | https://bio.tools/tcoffee, https://sources.debian.org/src/t-coffee/ | SCR_011818 | T-Coffee: Aligns DNA RNA or Proteins using the default T-Coffee | 2026-07-30 09:28:39 | 1121 | ||||||
|
ProbCons Resource Report Resource Website 100+ mentions |
ProbCons (RRID:SCR_011813) | ProbCons | service resource, production service resource, analysis service resource, data analysis service | Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Stanford University; Stanford; California |
PMID:15687296 DOI:10.1101/gr.2821705 |
OMICS_00986, biotools:probcons | https://bio.tools/probcons, https://sources.debian.org/src/probcons/ | SCR_011813 | ProbCons: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences | 2026-07-30 09:28:41 | 106 | ||||||
|
AceDB Resource Report Resource Website 10+ mentions |
AceDB (RRID:SCR_010671) | data or information resource, database, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software genome database management system. | genome database management system, genome database, management system, |
is listed by: Debian is listed by: OMICtools is related to: ESTHER has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
DOI:10.1109/5992.764215 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_75315, OMICS_15828 | https://sources.debian.org/src/acedb-other/ | SCR_010671 | A C. elegans DataBase | 2026-07-30 09:28:35 | 12 | ||||||
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FGENESH Resource Report Resource Website 100+ mentions |
FGENESH (RRID:SCR_011928) | FGENESH | service resource, production service resource, analysis service resource, data analysis service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fgenesh, OMICS_01483 | https://bio.tools/fgenesh | SCR_011928 | 2026-07-30 09:28:42 | 330 | |||||||
|
RACE Resource Report Resource Website 100+ mentions |
RACE (RRID:SCR_010950) | RACE | service resource, production service resource, analysis service resource, data analysis service | A collection of web tools designed to assist with the analysis of DNA microarray data and results. RACE performs probe level data preprocessing, quality checks, normalization, and visualization for Affymetrix GeneChips. In addition, it performs clustering and differential analysis of normalized expression levels or ratios for arbitrary platforms, and estimates the false discovery rates in lists of potentially regulated genes. A Gene Ontology (GO)-term analysis assists in the biological interpretation of gene lists. The user can customize each analysis request; upon submission the analysis is executed in a fully automated way., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | dna microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Lausanne; Lausanne; Switzerland |
PMID:15980552 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00777, biotools:race | https://bio.tools/race | SCR_010950 | Remote Analysis Computation for gene Expression data | 2026-07-30 09:28:39 | 357 | |||||
|
HSLPred Resource Report Resource Website |
HSLPred (RRID:SCR_011972) | HSLPred | service resource, production service resource, analysis service resource, data analysis service | A support vector machine (SVM)-based method for the prediction of 4 major subcellular localization (cytoplasm, mitochondrial, nuclear and plasma membrane) of human proteins using various features such as i) amino acid composition, ii) dipeptide composition and iii) evolutionary information of proteins. | subcellular localization, protein, support vector machine, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Institute of Microbial Technology; Chandigarh; India |
PMID:15647269 | Acknowledgement requested | biotools:hslpred, OMICS_01622 | https://bio.tools/hslpred | SCR_011972 | HSLPred - A SVM-based Method for Subcellular Localization of Human Proteins | 2026-07-30 09:28:43 | 0 | |||||
|
Pscan-ChIP Resource Report Resource Website 1+ mentions |
Pscan-ChIP (RRID:SCR_010885) | Pscan-ChIP | service resource, production service resource, analysis service resource, data analysis service | Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23748563 DOI:10.1093/nar/gkt448 |
biotools:pscanchip, OMICS_00490 | https://bio.tools/pscanchip, https://sources.debian.org/src/pscan-chip/ | SCR_010885 | 2026-07-30 09:28:37 | 5 | |||||||
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CUPSAT Resource Report Resource Website 50+ mentions |
CUPSAT (RRID:SCR_010773) | CUPSAT | service resource, production service resource, analysis service resource, data analysis service | A tool to predict changes in protein stability upon point mutations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16845001 | biotools:cupsat, OMICS_00128 | https://bio.tools/cupsat | SCR_010773 | Cologne University Protein Stability Analysis Tool, CUPSAT: Cologne University Protein Stability Analysis Tool | 2026-07-30 09:28:36 | 74 | ||||||
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LS-SNP/PDB Resource Report Resource Website 1+ mentions |
LS-SNP/PDB (RRID:SCR_010774) | LS-SNP/PDB | service resource, production service resource, analysis service resource, data analysis service | A web tool for genome-wide annotation of human SNPs. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA |
OMICS_00131, biotools:ls-snp | https://bio.tools/ls-snp | SCR_010774 | 2026-07-30 09:28:36 | 3 |
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