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http://code.google.com/p/chimerascan/
Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data.
Proper citation: chimerascan (RRID:SCR_013298) Copy
http://www.eisenlab.org/eisen/?page_id=42
Software to graphically browse results of clustering and other analyses from Cluster.
Proper citation: TreeView (RRID:SCR_013503) Copy
http://tiger.dbs.nus.edu.sg/cnv-seq/
A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CNV-seq (RRID:SCR_013357) Copy
http://huttenhower.sph.harvard.edu/galaxy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: LEfSe (RRID:SCR_014609) Copy
http://amp.pharm.mssm.edu/clustergrammer/
Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features.
Proper citation: clustergrammer (RRID:SCR_015681) Copy
http://technelysium.com.au/?page_id=13
Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Chromas (RRID:SCR_000598) Copy
https://ccg.murdoch.edu.au/yabi/login/?next=/yabi/
A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts.
Proper citation: Yabi (RRID:SCR_005359) Copy
A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.
Proper citation: RAST Server (RRID:SCR_014606) Copy
http://amphoranet.pitgroup.org/
Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample.
Proper citation: AmphoraNet (RRID:SCR_005009) Copy
http://katahdin.mssm.edu/kismeth/revpage.pl
A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species.
Proper citation: Kismeth (RRID:SCR_005444) Copy
http://genetrail.bioinf.uni-sb.de/
A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GeneTrail (RRID:SCR_006250) Copy
http://samtools.sourceforge.net/mpileup.shtml
Provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Proper citation: SAMtools/BCFtools (RRID:SCR_005227) Copy
Tool for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
Proper citation: Hmmer (RRID:SCR_005305) Copy
http://bioinformatics.ua.pt/becas/
Web application, API and widget able to recognize and annotate biomedical concepts in text.Provides annotations for isolated, nested and intersected entities.Identifies concepts from multiple semantic groups, providing preferred names and enriching them with references to public knowledge resources.
Proper citation: becas (RRID:SCR_005337) Copy
http://bioportal.bioontology.org/annotator
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.
Proper citation: NCBO Annotator (RRID:SCR_005329) Copy
http://services.nbic.nl/copub/portal/
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.
Proper citation: CoPub (RRID:SCR_005327) Copy
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.
Proper citation: PAZAR (RRID:SCR_005410) Copy
http://www.jcvi.org/cgi-bin/tigrfams/index.cgi
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.
Proper citation: TIGRFAMS (RRID:SCR_005493) Copy
http://www.bioinf.uni-leipzig.de/Software/segemehl/
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.
Proper citation: Segemehl (RRID:SCR_005494) Copy
A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.
Proper citation: Maq (RRID:SCR_005485) Copy
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