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https://code.google.com/p/mirpara/
A SVM (support vector machine-based software tool for prediction of most probable microRNA coding regions in genome scale sequences.
Proper citation: MiRPara (RRID:SCR_005294) Copy
http://www.scienceexchange.com/facilities/zyagen
A commercial service organization from Zyagen.
Proper citation: Zyagen (RRID:SCR_005295) Copy
https://github.com/songlab/chance
A standalone software package for ChIP-seq quality control and protocol optimization.
Proper citation: CHANCE (RRID:SCR_005330) Copy
Software using a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid discovery of errors and comparisons between similar assemblies.
Proper citation: Assembly Likelihood Estimator (RRID:SCR_005326) Copy
The German Institute for Economic Research or more commonly DIW Berlin is a economic research institute in Germany, involved in basic research and policy advice.
Proper citation: German Institute of Economic Research; Berlin; Germany (RRID:SCR_005320) Copy
http://purl.bioontology.org/ontology/CABRO
A web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living.
Proper citation: Computer Assisted Brain Injury Rehabilitation Ontology (RRID:SCR_005288) Copy
http://users-birc.au.dk/biopv/php/fabox/
Tools for splitting, joining and otherwise manipulating FASTA format sequence files. The first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison allowing users to combine the description of data (often in excel spreadsheets) with the actual data (often DNA sequences). Also, producing correct input files for a range of programs seems to be problematic for the average user. Hence, some converters in some of the services have been included as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you''ll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs. This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use. Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER.
Proper citation: FaBox (RRID:SCR_005350) Copy
A private, nonprofit, nonsectarian, Historically Black College and University and a Minority Serving Institution located in Willowbrook, unincorporated Los Angeles County, California, United States.
Proper citation: Charles R. Drew University of Medicine and Science; California; USA (RRID:SCR_005346) Copy
http://info.gersteinlab.org/PeakSeq
A software program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.
Proper citation: PeakSeq (RRID:SCR_005349) Copy
http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi
A web based search tool to help you gain an overview of the set of articles (up to 25,000 most recent articles) retrieved by a PubMed query. Once you enter a query, you can select different types of summary information to view: Important words, Topics, Authors, Affiliations, Journals, Year, Clustered by topic.
Proper citation: Anne O'Tate (RRID:SCR_005340) Copy
Java software for studying protein-DNA interaction using ChIP-seq / ChIP-exo data. It links binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence, resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution. GEM reciprocally improves motif discovery using binding event locations, and binding event predictions using discovered motifs.
Proper citation: GEM (RRID:SCR_005339) Copy
http://mirnylab.bitbucket.org/hiclib/index.html
An Software resource
Proper citation: Hiclib (RRID:SCR_005535) Copy
http://compbio.cs.toronto.edu/shrimp/
A software package for aligning genomic reads against a target genome.
Proper citation: SHRiMP (RRID:SCR_005496) Copy
http://www.sanger.ac.uk/resources/software/smalt/
Software that aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads.
Proper citation: SMALT (RRID:SCR_005498) Copy
http://www.enseignementsup-recherche.gouv.fr/
Ministry of Higher Education, Research and Innovation, France is one of the 900 Higher Education-related Organizations and Associations.
Proper citation: French Ministry of Higher Education and Research (RRID:SCR_005532) 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
http://pass.cribi.unipd.it/cgi-bin/pass.pl
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PASS (RRID:SCR_005490) Copy
Governmental agency of Italy. Its headquarters are in Rome and is led by the Italian Minister of Health.
Proper citation: Ministry of Health; Rome; Italy (RRID:SCR_005526) Copy
http://pythonhosted.org/pyDNase/
A software library for analyzing DNase-seq data.
Proper citation: pyDNase (RRID:SCR_005406) Copy
http://pringlelab.stanford.edu/projects.html
Software to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.
Proper citation: Fulcrum (RRID:SCR_005523) Copy
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