Tools   Select Another Resource Report Type

https://github.com/zd1/telseq

Software that measures average telomere length from whole genome or exome shotgun sequence data.

Proper citation: TelSeq (RRID:SCR_002730) Copy   

•   Source: SciCrunch Registry
  

https://www.innopsys.com/en/lifesciences-products/microarrays/software

System control software used for data acquisition and analysis for microarray images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Mapix (RRID:SCR_002723) Copy   

•   Source: SciCrunch Registry
  

http://swift.cmbi.ru.nl/gv/dssp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries. DSSP is distributed on a basis of trust and instructions are available on the site. * Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt * Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code. * FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command.

Proper citation: Database of Secondary Structure Assignments (RRID:SCR_002725) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ahmohamed/NetPathMiner

Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths.

Proper citation: NetPathMiner (RRID:SCR_002757) Copy   

•   Source: SciCrunch Registry
  

http://yu68.github.io/GATE/

Model-based, open source software analysis tool for chromatin states prediction based on time-course epigenetic marks data. It uses a combinatory Finite Mixture model nested with HMM to model the time course marks data in which each single hidden markov model describes the hidden states for a region set across different time points.

Proper citation: GATE (RRID:SCR_002756) Copy   

•   Source: SciCrunch Registry
  

http://www.cisd.ethz.ch/software/openBIS

Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics

Proper citation: openBIS (RRID:SCR_011815) Copy   

•   Source: SciCrunch Registry
  

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

A fast and accurate multiple sequence alignment algorithm.

Proper citation: Kalign (RRID:SCR_011810) Copy   

•   Source: SciCrunch Registry
  

http://mafft.cbrc.jp/alignment/server/

Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.

Proper citation: MAFFT (RRID:SCR_011811) Copy   

•   Source: SciCrunch Registry
  

http://wishart.biology.ualberta.ca/cgview/

A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CGView (RRID:SCR_011779) Copy   

•   Source: SciCrunch Registry
  

http://bioen-compbio.bioen.illinois.edu/PSAR-Align/

Software for improving multiple sequence alignment using probabilistic sampling.

Proper citation: PSAR-Align (RRID:SCR_011814) Copy   

•   Source: SciCrunch Registry
  

http://gaggle.systemsbiology.net/docs/geese/genomebrowser/

An open source software tool for visualizing high-density data plotted against coordinates on the genome.

Proper citation: Gaggle (RRID:SCR_011780) Copy   

•   Source: SciCrunch Registry
  

http://www.csd.uwo.ca/~ilie/HiTEC/

Accurate error correction in high-throughput sequencing data.

Proper citation: HiTEC (RRID:SCR_011826) Copy   

•   Source: SciCrunch Registry
  

https://bioinf.eva.mpg.de/patman/

Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PatMaN (RRID:SCR_011821) Copy   

•   Source: SciCrunch Registry
  

http://bix.ucsd.edu/projects/hammer/

A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Hammer (RRID:SCR_011825) Copy   

•   Source: SciCrunch Registry
  

http://www.g-language.org/GenomeProjector/

A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.

Proper citation: Genome Projector (RRID:SCR_011790) Copy   

•   Source: SciCrunch Registry
  

https://hci-bio-app.hci.utah.edu/gnomex/

A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets.

Proper citation: GNomEx (RRID:SCR_011805) Copy   

•   Source: SciCrunch Registry
  

http://infernal.janelia.org/

Software for searching DNA sequence databases for RNA structure and sequence similarities.

Proper citation: Infernal (RRID:SCR_011809) Copy   

•   Source: SciCrunch Registry
  

http://www.ige.tohoku.ac.jp/joho/gmProject/gmhome.html

A graphical interface for comparative genomics.

Proper citation: GenomeMatcher (RRID:SCR_011800) Copy   

•   Source: SciCrunch Registry
  

http://www-ps.informatik.uni-tuebingen.de/itNew/?page_id=1160

Alignment visualization based on SuperGenome coordinates.

Proper citation: GenomeRing (RRID:SCR_011801) Copy   

•   Source: SciCrunch Registry
  

http://try-gobe.appspot.com/

An interactive, web-based tool for comparative genomic visualization.

Proper citation: Gobe (RRID:SCR_011802) Copy   

•   Source: SciCrunch Registry