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http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl

A database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains >2000 samples from >500 ChIP-seq and ChIP-chip experiments, representing a total of >170 proteins and >10,000,000 protein-DNA interactions (March 2014). A web server provides an interface for database query. Protein-DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell type dependencies, and cross-sample variability of protein-DNA interactions.

Proper citation: hmChIP (RRID:SCR_005407) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/lib/chea.jsp

Data analysis service for gene-list enrichment analysis against a manual database. It allows users to input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The database integrates interaction data from ChIP-chip, ChIP-seq, ChIP-PET and DamID studies and contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes.

Proper citation: ChEA (RRID:SCR_005403) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hadoop-bam/

A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF.

Proper citation: Hadoop-BAM (RRID:SCR_005516) Copy   

•   Source: SciCrunch Registry

http://sb.cs.cmu.edu/seecer/

Algorithm for sequencing error correction of RNA-seq data sets. SEECER removes mismatch and indel errors from the raw reads and improves downstream analysis of the data.

Proper citation: SEECER (RRID:SCR_005274) Copy   

•   Source: SciCrunch Registry

http://htseq.readthedocs.io/en/release_0.9.1/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.

Proper citation: HTSeq (RRID:SCR_005514) Copy   

•   Source: SciCrunch Registry

http://www.gene-talk.de

A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations.

Proper citation: GeneTalk (RRID:SCR_005231) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/msa/muscle/

Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation.

Proper citation: MUSCLE (RRID:SCR_011812) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-genomics-workbench/

Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program.

Proper citation: CLC Genomics Workbench (RRID:SCR_011853) Copy   

•   Source: SciCrunch Registry

http://gwyddion.net/

Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry.

Proper citation: Gwyddion (RRID:SCR_015583) Copy   

•   Source: SciCrunch Registry

http://the_brain.bwh.harvard.edu/uniprobe/

Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences.

Proper citation: UniPROBE (RRID:SCR_005803) Copy   

•   Source: SciCrunch Registry

http://mutationassessor.org/

A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MutationAssessor (RRID:SCR_005762) Copy   

•   Source: SciCrunch Registry

http://gopubmed.org/web/gopubmed/

A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool

Proper citation: GoPubMed (RRID:SCR_005823) Copy   

•   Source: SciCrunch Registry

http://agbase.msstate.edu/cgi-bin/tools/goslimviewer_select.pl

Service to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs.

Proper citation: GOSlimViewer (RRID:SCR_005665) Copy   

•   Source: SciCrunch Registry

http://pipeclip.qbrc.org/

A Galaxy framework-based online pipeline for reliable analysis of data generated by three types of CLIP-seq protocols: HITS-CLIP, PAR-CLIP and iCLIP. It provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PIPE-CLIP (RRID:SCR_005820) Copy   

•   Source: SciCrunch Registry

http://mint.bio.uniroma2.it/virusmint/

A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome.

Proper citation: VirusMINT (RRID:SCR_005987) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org

International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.

Proper citation: Mouse Genome Informatics (MGI) (RRID:SCR_006460) Copy   

•   Source: SciCrunch Registry

http://panoga.sabanciuniv.edu/

A web server to devise functionally important pathways through the identification of single nucleotide polymorphism (SNP)-targeted genes within these pathways. The strength of the methodology stems from its multidimensional perspective, where evidence from the following five resources is combined: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein-protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways.

Proper citation: PANOGA (RRID:SCR_006242) Copy   

•   Source: SciCrunch Registry

http://tardis.nibio.go.jp/homstrad/

A curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER. These structure-based alignments are annotated with JOY and examined individually.

Proper citation: HOMSTRAD - Homologous Structure Alignment Database (RRID:SCR_006544) Copy   

•   Source: SciCrunch Registry

http://gtlinker.cnb.csic.es/

Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service.

Proper citation: GeneTerm Linker (RRID:SCR_006385) Copy   

•   Source: SciCrunch Registry

http://www.nactem.ac.uk/medie/

An intelligent search engine to retrieve biomedical correlations from MEDLINE, based on indexing by Natural Language Processing and Text Mining techniques. You can find abstracts/sentences in MEDLINE by specifying semantics of correlations; for example, What activates p53 and What causes colon cancer. Semantic search uses a semantic query for finding biomedical correlations. Input a subject, a verb, and an object of a concept (or either of them) into a form. Results of the query will be shown in a second. (E.g., What does p53 activate? (subject=p53, verb=activate)) Reference: Miyao, Yusuke, Tomoko Ohta, Katsuya Masuda, Yoshimasa Tsuruoka, Kazuhiro Yoshida, Takashi Ninomiya and Jun''''ichi Tsujii (2006) Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. Proceedings COLING-ACL 2006. Sydney, Australia, pp. 1017--1024.

Proper citation: MEDIE (RRID:SCR_006254) Copy   

•   Source: SciCrunch Registry