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http://fulxie.0fees.us/?type=reference&ckattempt=1

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RefFinder (RRID:SCR_000472) Copy   

•   Source: SciCrunch Registry

http://trace.ddbj.nig.ac.jp/dor/index_e.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy.

Proper citation: DDBJ Omics Archive (RRID:SCR_000597) Copy   

•   Source: SciCrunch Registry

http://www.atgc-montpellier.fr/mpscan/

Web tool for index free mapping of multiple short reads on a genome.

Proper citation: MPscan (RRID:SCR_000587) Copy   

•   Source: SciCrunch Registry

http://gowiki.tamu.edu/wiki/

A wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms. The rationale for this wiki is based on helping new users of the gene ontology understand and use it. The GONUTS wiki is not an official product of the the Gene Ontology consortium. The GO consortium has a public wiki at their website, http://wiki.geneontology.org/. Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker. However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages. Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology. GONUTS is currently set up so anyone can view or search, but only registered users can edit or add pages. Currently registered users can create new users, and we are working to add at least one registered user for each participating database (So far we have registered users at EcoliHub, EcoCyc, GOA, BeeBase, SGD, dictyBase, FlyBase, WormBase, TAIR, Rat Genome Database, ZFIN, MGI, UCL and AgBase...

Proper citation: GONUTS (RRID:SCR_000653) Copy   

•   Source: SciCrunch Registry

http://edwards.sdsu.edu/scaffold_builder/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.

Proper citation: Scaffold builder (RRID:SCR_000556) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/bamseek/

A Large File Viewer for BAM and SAM alignment files.

Proper citation: BAMseek (RRID:SCR_000672) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/popbam/

A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.

Proper citation: POPBAM (RRID:SCR_000464) Copy   

•   Source: SciCrunch Registry

http://bsec.ornl.gov/AdaptiveCrawler.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers.

Proper citation: AdaptiveCrawler (RRID:SCR_000573) Copy   

•   Source: SciCrunch Registry

http://bcbio.wordpress.com/

This blog will appeal to those dealing with the practical day to day work of biological data analysis and presentation.

Proper citation: Blue Collar Bioinformatics (RRID:SCR_012913) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/ena/search/

A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity.

Proper citation: ENA Sequence Search (RRID:SCR_013170) Copy   

•   Source: SciCrunch Registry

http://www.benoslab.pitt.edu/comir/

Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.

Proper citation: ComiR (RRID:SCR_013023) Copy   

•   Source: SciCrunch Registry

http://www.hsls.pitt.edu/

Database access to information services, educational opportunities, and resources in print and electronic format to faculty, students, and researchers in the schools of the health sciences.

Proper citation: University of Pittsburgh, Health Sciences Library System (RRID:SCR_011975) Copy   

•   Source: SciCrunch Registry

http://omabrowser.org/cgi-bin/gateway.pl

A database that identifies orthologs among publicly available, complete genomes. It offers a comprehensive search and numerous display options for 4.7 million proteins from 1000 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed.

Proper citation: OMA Browser (RRID:SCR_011978) Copy   

•   Source: SciCrunch Registry

http://gsgator.ewha.ac.kr/

A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks.

Proper citation: gsGator (RRID:SCR_012035) Copy   

•   Source: SciCrunch Registry

https://www.orthodb.org/

Database of orthologous protein coding genes across vertebrates, arthropods, fungi, basal metazoans, and bacteria.

Proper citation: OrthoDB (RRID:SCR_011980) Copy   

•   Source: SciCrunch Registry

http://core-genomics.blogspot.de/

This blog focusses on next-generation sequencing and microarray technologies.

Proper citation: CoreGenomics (RRID:SCR_011985) Copy   

•   Source: SciCrunch Registry

http://www.bio-itworld.com/

A leading source of news on technology and innovation in life sciences IT, informatics, genomics, next-gen, drug discovery, development, and clinical trials.

Proper citation: Bio-IT World (RRID:SCR_011986) Copy   

•   Source: SciCrunch Registry

http://www.genoread.org/

A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence.

Proper citation: GenoREAD (RRID:SCR_012007) Copy   

•   Source: SciCrunch Registry

http://cdwscience.blogspot.fr/

A blog about genetics, genomics, and medical research.

Proper citation: My Biomedical Informatics Blog (RRID:SCR_012011) Copy   

•   Source: SciCrunch Registry

http://cbbiweb.uthscsa.edu/KMethylomes/

Datbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers.

Proper citation: Cancer Methylome System (RRID:SCR_012013) Copy   

•   Source: SciCrunch Registry