Curator Dashboard

Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.

• Resource
• SciCrunch
• 9 years ago - submitted by Bruno Contreras-Moreira

Web application for structural alignment of DNA motifs and protein domains from DNA binding protein complexes in Protein Data Bank.

• Resource
• SciCrunch
• 9 years ago - submitted by Bruno Contreras-Moreira

Web application for predicting transcription factors which bind a specific DNA site or motif, as well as DNA motifs or sites likely to be recognized by a specific DNA-binding protein. footprintDB also lists several databases and repositories relevant to DNA transcription.

• Resource
• SciCrunch
• 9 years ago - submitted by Bruno Contreras-Moreira

Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map and the POPSEQ map. Its three main functions are finding markers, aligning sequences, and locating by position.

• Resource
• SciCrunch
• 9 years ago - submitted by Bruno Contreras-Moreira

Perl software script that can annotate barley sequences with Gene Ontology terms inferred by homology. It uses the IBSC2012 barley GO annotation and supports both nucleotide and peptide sequences.

• Resource
• SciCrunch
• 9 years ago - submitted by Bruno Contreras-Moreira

Open source software to evaluate, quantify, compare, and predict the metabolic machinery of interest in large ‘omic’ datasets. This protocol finds informative protein families and uses them to score metagenomic sets.

• Resource
• SciCrunch
• 9 years ago - submitted by Valerie De Anda

Software for processing NGS sequence reads in FASTQ and FASTA formats. split_pairs.pl is suited particularly for the task of sorting pair end reads and for modifying their headers with Perl-style regular expressions.

• Resource
• SciCrunch
• 9 years ago - submitted by Bruno Contreras-Moreira

Software scripts for the assembly of chloroplast genomes out of whole-genome sequencing reads.

• Resource
• SciCrunch
• 9 years ago - submitted by Bruno Contreras-Moreira

Software package for pan-genome analysis. This software is suitable for bacterial genomes and the study of intra-specific eukaryotic pan-genomes.

• Resource
• SciCrunch
• 9 years ago - submitted by Bruno Contreras-Moreira

Software for processing, display, and analysis of magnetic resonance spectroscopic imaging data. MIDAS supports a "whole-brain" MRSI acquisition method that has been implemented on MRI systems from three major manufacturers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• RRID-Legacy
• 9 years ago - by Anonymous

Software for image analysis, processing and quantitation. This software analyzes standard JPEG, BMP, PNG, TIFF images; 16-bit TIFF images; and .GEL files produced by Phosphorimager, Typhoon and Storm instruments.

• Resource
• RRID-Legacy
• 9 years ago - submitted by Anita Bandrowski

Data set of thalamo-centric mesoscopic projection maps to the cortex and striatum. The maps are established through two-color, viral (rAAV)-based tracing images and high throughout imaging.

• Resource
• RRID-Legacy
• 9 years ago - by Anonymous

Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

• Resource
• RRID-Legacy
• 9 years ago - by Anonymous

Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions.

• Resource
• RRID-Legacy
• 9 years ago - by Anonymous

Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code.

• Resource
• SciCrunch
• 9 years ago - submitted by James Go

Kit for assessing motor function and endurance in mice and rats. IITC’s Rotarod Test is capable of having up to five mice or rats tested at a time standard.

• RRID-Legacy
• 9 years ago - submitted by Neil Ford

A script to convert Bam alignments into a wig representation file.

• Resource
• RRID-Legacy
• 9 years ago - by Anonymous

Tools for querying and analysis of genomic data. These libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined regions of interest (epigenetic enrichment, transcription factor binding sites, etc.). This library works with these tables and provides a set of common tools for working with them. Opening and saving common tab-delimited text formats Support for BED, GFF, VCF, narrowPeak files Scoring intervals with datasets from microarray and sequencing ChIPSeq, RNASeq, microarray expression Support for Bam, BigWig, BigBed, wig, and USeq data formats Intersection with other known annotation Works with any genomic annotation in GTF, GFF3, and UCSC formats The libraries provide a unified and integrated approach to analyses. In many cases, they provide an abstraction layer over a variety of different specialized BioPerl and related modules. Instead of writing numerous scripts specialized for each data format (wig, bigWig, Bam), one script can now work with any data format.

• Resource
• RRID-Legacy
• 9 years ago - by Anonymous

A commercial software package that works with Carl Zeiss microscopy; AIM 4.2 software.

• Resource
• RRID-Legacy
• 9 years ago - by Anonymous

A variant vcf file analysis tool.

• Resource
• RRID-Legacy
• 9 years ago - by Anonymous