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on page 1 showing 20 out of 305 results

    4Peaks

Cite this (4Peaks, RRID:SCR_000015)

URL: http://nucleobytes.com/index.php/4peaks

Resource Type: Resource, software resource, software application

Software application for viewing and editing sequence trace files.

  • From Current Category

Cite this (AbsCN-seq, RRID:SCR_006409)

URL: http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Resource Type: Resource, software resource

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

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Cite this (AbundanceBin, RRID:SCR_004648)

URL: http://omics.informatics.indiana.edu/AbundanceBin/

Resource Type: Resource, software resource

An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community.

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Cite this (AbundantOTU+, RRID:SCR_016527)

URL: http://omics.informatics.indiana.edu/AbundantOTU/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.

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    ADaCGH

Cite this (ADaCGH, RRID:SCR_010916)

URL: http://adacgh.bioinfo.cnio.es/

Resource Type: Resource, analysis service resource, software resource, data analysis service, service resource, production service resource

A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/

  • From Current Category

Cite this (Advanced Sequence Automated Pipeline, RRID:SCR_005578)

URL: http://biostat.mc.vanderbilt.edu/wiki/Main/ASAP

Resource Type: Resource, software resource

Software developed to provide a framework for building and executing a pipeline to preprocess next generation sequence data and variant calls.

  • From Current Category

    AffinDB

Cite this (AffinDB, RRID:SCR_001690)

URL: http://pc1664.pharmazie.uni-marburg.de/affinity/

Resource Type: Resource, data or information resource, database

Database of affinity data for protein-ligand complexes of the Protein Data Bank (PDB) providing direct and free access to the experimental affinity of a given complex structure. Affinity data are exclusively obtained from the scientific literature. As of Thursday, May 01st, 2014, AffinDB contains 748 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex. AffinDB provides access to data in three different forms:
# Summary information for PDB entry
# Affinity information window
# Tabular reports

  • From Current Category

Cite this (AlienTrimmer, RRID:SCR_011835)

URL: ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/

Resource Type: Resource, software resource

Allows detecting and removing multiple alien sequences in both ends of sequence reads.

  • From Current Category

Cite this (Align-GVGD, RRID:SCR_010772)

URL: http://agvgd.iarc.fr/index.php

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral.

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    AllSeq

Cite this (AllSeq, RRID:SCR_010053)

URL: http://www.allseq.com/default.aspx

Resource Type: Resource, service resource

Free online tools to find the best Sequencing Service provider for your project.

  • From Current Category

Cite this (AltAnalyze - Alternative Splicing Analysis Tool, RRID:SCR_002951)

URL: http://www.altanalyze.org/

Resource Type: Resource, software resource, software application

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

  • From Current Category

Cite this (AmphoraNet, RRID:SCR_005009)

URL: http://amphoranet.pitgroup.org/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample.

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Cite this (AnalyzeReplication, RRID:SCR_012030)

URL: http://home.uchicago.edu/~jiezhou/replication/

Resource Type: Resource, software resource

Source code providing a cost-effectiveness metric for guiding the design of large-scale RNA-seq differentially expressed (DE) studies.

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    APPRIS

Cite this (APPRIS, RRID:SCR_012019)

URL: http://appris.bioinfo.cnio.es/

Resource Type: Resource, data or information resource, database

A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript.

  • From Current Category

Cite this (Arabidopsis Gene Regulatory Information Server, RRID:SCR_006928)

URL: http://arabidopsis.med.ohio-state.edu

Resource Type: Resource, data or information resource, database

An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB).

  • From Current Category

Cite this (Arabidopsis thaliana Protein Interactome Database, RRID:SCR_001896)

URL: http://www.megabionet.org/atpid/webfile/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.

  • From Current Category

Cite this (ARB project, RRID:SCR_000515)

URL: http://www.arb-home.de/

Resource Type: Resource, software resource

A software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. The programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. The ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. The majority of operations can be controlled using the mouse for moving the pointer and the left mouse button for initiating and performing operations.

  • From Current Category

Cite this (Argo Genome Browser, RRID:SCR_011763)

URL: http://www.broadinstitute.org/annotation/argo/

Resource Type: Resource, software resource, data set, data or information resource

A tool for visualizing and manually annotating whole genomes that can be run as Applet or Webstart application as well as standalone application.

  • From Current Category

Cite this (ArrayOligoSelector, RRID:SCR_013494)

URL: http://arrayoligosel.sourceforge.net/

Resource Type: Resource, software resource

Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene.

  • From Current Category

Cite this (ArrayQuest, RRID:SCR_010935)

URL: http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web-accessible program for the analysis of DNA microarray data. ArrayQuest is designed to apply any type of DNA microarray analysis program executable on a Linux system (i.e., Bioconductor statistical and graphical methods written in R as well as BioPerl and C++ based scripts) to DNA microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or in a password protected private database uploaded to the center point server. ArrayQuest analyses are performed on a computer cluster.

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