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Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.
Proper citation: Distant Regulatory Elements (RRID:SCR_003058) Copy
https://github.com/cmayer/BaitFisher-package
Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.
Proper citation: Baitfisher (RRID:SCR_015985) Copy
Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Proper citation: Avogadro (RRID:SCR_015983) Copy
https://github.com/sanger-pathogens/Bio-Tradis
Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.
Proper citation: Bio-tradis (RRID:SCR_015993) Copy
http://www.vicbioinformatics.com/software.barrnap.shtml
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Barrnap (RRID:SCR_015995) Copy
Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences.
Proper citation: Fastml (RRID:SCR_016092) Copy
http://standage.github.io/AEGeAn
Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.
Proper citation: Aegean (RRID:SCR_015965) Copy
https://github.com/EvolBioInf/andi
Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.
Proper citation: andi (RRID:SCR_015971) Copy
Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences.
Proper citation: Garlic (RRID:SCR_016118) Copy
Software application which provides a graphical interface to build, view and analyze atomic structures. It provides a graphical interface to study atomic structures, to prepare images for presentations, and teach the atomic structure of matter.
Proper citation: Gamgi (RRID:SCR_016116) Copy
http://disulfind.dsi.unifi.it/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.
Proper citation: DISULFIND (RRID:SCR_016072) Copy
https://bitbucket.org/vboza/deepnano
Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate.
Proper citation: DeepNano (RRID:SCR_016070) Copy
Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TreeDyn (RRID:SCR_015946) Copy
https://github.com/PacificBiosciences/FALCON
Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.
Proper citation: Falcon (RRID:SCR_016089) Copy
http://genome.imim.es/software/gfftools/GFF2APLOT.html
Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis.
Proper citation: Gff2aplot (RRID:SCR_016128) Copy
http://bioconductor.org/packages/release/bioc/html/SC3.html
Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.
Proper citation: SC3 (RRID:SCR_015953) Copy
Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.
Proper citation: Gentle (RRID:SCR_016127) Copy
https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Exonerate (RRID:SCR_016088) Copy
http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMALIGN
Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.
Proper citation: DOMALIGN (RRID:SCR_016085) Copy
https://github.com/osallou/cassiopee-c
Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.
Proper citation: Cassiopee (RRID:SCR_016056) Copy
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