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http://mgc.nci.nih.gov/

NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).

Proper citation: Mammalian Gene Collection (RRID:SCR_007024) Copy   

•   Source: SciCrunch Registry

http://www.biorep.it/en

Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories.

Proper citation: BioRep (RRID:SCR_004907) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/TMHMM/

Web application for the prediction of transmembrane helices in proteins using Hidden Markov Models. FASTA formatted sequences can be uploaded via file or copy-paste, and output can be formatted as extensive with graphics, extensive without graphics, or one line per protein. Submissions are limited to 10,000 sequences and 4,000,000 amino acids - each sequence is limited to no more than 8,000 amino acids.

Proper citation: TMHMM Server (RRID:SCR_014935) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/ProP/

Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.

Proper citation: ProP Server (RRID:SCR_014936) Copy   

•   Source: SciCrunch Registry

http://www.cprofiler.org/

Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.

Proper citation: Composition Profiler (RRID:SCR_014630) Copy   

•   Source: SciCrunch Registry

http://www.glycosciences.de/tools/GlycoFragments/

Service that calculates and displays the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MS-spectra. The extended ASCII nomenclature as recommended by IUPAC is used to input the sequence of complex oligosaccharides. However, some additional input rules have to be fulfilled. In case only the topology and composition of the oligosaccharide is known, a simpler way to input carbohydrate sequences is possible. Since the hydroxyl groups of synthetic carbohydrates are often the are protected they have included a way to indicate if sugar residue are persubstituted. Please have a look at the examples of valid input structures.

Proper citation: GlycoFragment (RRID:SCR_001573) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/services/DictyOGlyc-1.1/

Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.

Proper citation: DictyOGlyc (RRID:SCR_001600) Copy   

•   Source: SciCrunch Registry

http://mirna.imbb.forth.gr/SSCprofiler.html

Tool which can be used to identify novel miRNA gene candidates in the human genome.

Proper citation: SSCprofiler (RRID:SCR_001282) Copy   

•   Source: SciCrunch Registry

http://www.proweb.org/coddle/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene.

Proper citation: Coddle-Codons Optimized to Discover Deleterious LEsions (RRID:SCR_003003) Copy   

•   Source: SciCrunch Registry

http://bisearch.enzim.hu

BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification.

Proper citation: BiSearch: Primer Design and Search Tool (RRID:SCR_002980) Copy   

•   Source: SciCrunch Registry

http://diyhpl.us/~bryan/irc/protocol-online/protocol-cache/TFSEARCH.html

The TFSEARCH searches highly correlated sequence fragments against TFMATRIX transcription factor binding site profile database in the "TRANSFAC" databases developed at GBF-Braunschweig, Germany. The TFSEARCH program was written by Yutaka Akiyama (Kyoto University, currently at RWCP) in 1995.

Proper citation: TFSEARCH: Searching Transcription Factor Binding Sites (RRID:SCR_004262) Copy   

•   Source: SciCrunch Registry

http://metagenomics.anl.gov/

An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples.

Proper citation: MG-RAST (RRID:SCR_004814) Copy   

•   Source: SciCrunch Registry

http://www.umd.be/HSF3/

Software tool to help study pre-mRNA splicing and to better understand intronic and exonic mutations leading to splicing defects. To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, they have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-? and 9G8.

Proper citation: Human Splicing Finder (RRID:SCR_005181) Copy   

•   Source: SciCrunch Registry

http://athina.biol.uoa.gr/PRED-CLASS/

A system of cascading neural networks that classifies any protein, given its amino acid sequence alone, into one of four possible classes: membrane, globular, fibrous, mixed.

Proper citation: PRED-CLASS (RRID:SCR_006216) Copy   

•   Source: SciCrunch Registry

http://probeexplorer.cicancer.org/principal.php

Probe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query. Platform: Online tool

Proper citation: ProbeExplorer (RRID:SCR_007116) Copy   

•   Source: SciCrunch Registry

http://www.imtech.res.in/raghava/bhairpred/

Bhairpred server is based on machine learning technique SVM using single sequence information, evolutionary profile, predicted and observed secondary structure (as obtained using Psipred and DSSP), predicted and observed accessibility values (as obtainned from Netasa and DSSP). The methods were trained and tested on dataset of 2880 proteins and their performance was evaluated on dataset of 534 proteins used by Thornton (PNAS, 2002). Best prediction results were obtained with hybrid approach that combined prediction results from evolutionary profile, predicted secondary structure and accessibility.

Proper citation: SVM based method for predicting beta hairpin structures in proteins (RRID:SCR_008349) Copy   

•   Source: SciCrunch Registry

http://www.medinfopoli.polimi.it/GFINDer/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results.

Proper citation: GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) Copy   

•   Source: SciCrunch Registry

http://bioinfo2.ugr.es/IsoF/isofinder.html

Isofinder is an algorithm running on the web able to predict isochores at the sequence level. Isochores are long genome segments homogeneous in G+C. The algorithm works by moving a sliding pointer from left to right along the DNA sequence and computing the mean G+C values to the left and to the right of the pointer at each point. Additionally, the program checks whether this significance exceeds a probability threshold. If so, the sequence is cut at this point into two subsequences; otherwise, the sequence remains undivided. The procedure continues recursively for each of the two resulting subsequences created by each cut. This leads to the decomposition of a chromosome sequence into long homogeneous genome regions (LHGRs) with well-defined mean G+C contents, each significantly different from the G+C contents of the adjacent LHGRs. Most LHGRs can be identified with Bernardi''s isochores, given their correlation with biological features such as gene density, SINE and LINE (short, long interspersed repetitive elements) densities, recombination rate or single nucleotide polymorphism variability. The resulting isochore maps are available at http://bioinfo2.ugr.es/isochores/, and also at the UCSC Genome Browser (http://genome.cse.ucsc.edu/). Sponsors: Isofinder is funded by Universidad de Granada, Spain.

Proper citation: Isofinder: Isochore Computational Prediction (RRID:SCR_008342) Copy   

•   Source: SciCrunch Registry

http://tree.bio.ed.ac.uk/software/seqgen/

Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.

Proper citation: Seq-Gen (RRID:SCR_014934) Copy   

•   Source: SciCrunch Registry

http://www.vivo.colostate.edu/molkit/manip/#

A software tool that allows users to input a DNA (or RNA) sequence and obtain its inverse, complement or inverse complement. The program can also be used to display a DNA sequence and its complement in double-stranded format. Functions after users paste a DNA sequence into the upper text box, then click the appropriate button to place a manipulated form of the sequence in the lower text box.

Proper citation: Manipulate and Display a DNA Sequence (RRID:SCR_013470) Copy   

•   Source: SciCrunch Registry