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http://bioconductor.org/packages/release/bioc/html/flipflop.html

Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.

Proper citation: FlipFlop (RRID:SCR_000625) Copy   

•   Source: SciCrunch Registry

Discontinued

https://github.com/PacificBiosciences/blasr

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BLASR (RRID:SCR_000764) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gmcloser/

Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.

Proper citation: GMcloser (RRID:SCR_000646) Copy   

•   Source: SciCrunch Registry

https://github.com/shinout/clipcrop

Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files.

Proper citation: clipcrop (RRID:SCR_000678) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/triagetools/

A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.

Proper citation: TriageTools (RRID:SCR_000675) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/operasf/

A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

Proper citation: Opera (RRID:SCR_000665) Copy   

•   Source: SciCrunch Registry

http://toppcluster.cchmc.org/

A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.

Proper citation: ToppCluster (RRID:SCR_001503) Copy   

•   Source: SciCrunch Registry

http://statalign.github.io/

Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java.

Proper citation: StatAlign (RRID:SCR_001892) Copy   

•   Source: SciCrunch Registry

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

Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/

Proper citation: FACTA+. (RRID:SCR_001767) Copy   

•   Source: SciCrunch Registry

https://github.com/ndaniel/fusioncatcher

Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

Proper citation: FusionCatcher (RRID:SCR_000060) Copy   

•   Source: SciCrunch Registry

http://dissect-trans.sourceforge.net/Home

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.

Proper citation: Dissect (RRID:SCR_000058) Copy   

•   Source: SciCrunch Registry

https://cpndb.ca/

A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.

Proper citation: cpnDB: A Chaperonin Database (RRID:SCR_002263) Copy   

•   Source: SciCrunch Registry

http://www.predictprotein.org/

Web application for sequence analysis and the prediction of protein structure and function. The user interface intakes protein sequences or alignments and returned multiple sequence alignments, motifs, and nuclear localization signals., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Predictions for Entire Proteomes (RRID:SCR_002803) Copy   

•   Source: SciCrunch Registry

http://regulondb.ccg.unam.mx/

Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.

Proper citation: RegulonDB (RRID:SCR_003499) Copy   

•   Source: SciCrunch Registry

http://www.proteomexchange.org

A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas.

Proper citation: ProteomeXchange (RRID:SCR_004055) Copy   

•   Source: SciCrunch Registry

http://genome.unmc.edu/ngLOC/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License.

Proper citation: ngLOC (RRID:SCR_003150) Copy   

•   Source: SciCrunch Registry

https://www.biodiscovery.com/search/node?keys=Imagene

Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImaGene (RRID:SCR_002178) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.nl/QualitySNPng/

Software for the detection and visualization of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy.

Proper citation: QualitySNPng (RRID:SCR_002479) Copy   

•   Source: SciCrunch Registry

http://crdd.osdd.net/servers/virsirnadb/

VIRsiRNAdb is a curated database of experimentally validated viral siRNA / shRNA targeting diverse genes of 42 important human viruses including influenza, SARS and Hepatitis viruses. Submissions are welcome. Currently, the database provides detailed experimental information of 1358 siRNA/shRNA which includes siRNA sequence, virus subtype, target gene, GenBank accession, design algorithm, cell type, test object, test method and efficacy (mostly quantitative efficacies). Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. The database has facilities like search, advance search (using Boolean operators AND, OR) browsing (with data sorting option), internal linking and external linking to other databases (Pubmed, Genbank, ICTV). Additionally useful siRNA analysis tools are also provided e.g. siTarAlign for aligning the siRNA sequence with reference viral genomes or user defined sequences. virsiRNAdb would prove useful for RNAi researchers especially in siRNA based antiviral therapeutics development.

Proper citation: VIRsiRNAdb (RRID:SCR_006108) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.8/bioc/html/qrqc.html

Software R package to quickly scan reads and gather statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.

Proper citation: qrqc (RRID:SCR_006867) Copy   

•   Source: SciCrunch Registry