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BLASTN logo
search nucleotide subjects using a nucleotide query
Category: DNA alignment
Subcategories: NCBI

BLAST nucleotide (BLASTN) searches nucleotide subjects using a nucleotide query. Registration not required.

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TF Search logo
searching transcription factor binding sites

Given a DNA sequence, TF Search returns potential transcriptional factor binding sites on the sequence. Registration not required.

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Tfsitescan logo
promoter sequence analysis

Tfsitescan is intended for promoter sequence analysis and works best with sequences of ~500 nt Registration not required.

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TFBIND logo

TFBIND for online searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)). This tool uses weight matrix in transcription factor database TRANSFAC R.3.4 developed by Dr. Wingender et al, and the cut-offs originally estimated by our research. Registration not required.

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TRAP (single sequence) logo

TRAP (Transcription factor Affinity Prediction) is a web tool to predict which transcription factors are susceptible to bind a DNA sequence (e.g. promotor of a gene of interest) Registration not required.

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Pubmed logo
a free database accessing the MEDLINE database of citations, abstracts and some full text articles on life sciences and biomedical topics
Subcategories: NCBI

PubMed is a free database accessing the MEDLINE database of citations, abstracts and some full text articles on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health (NIH) maintains PubMed as part of the Entrez information retrieval system. Listing an article or journal in PubMed is not endorsement. Registration not required.

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Promo logo

PROMO (Alggen) is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. TFBS defined in the TRANSFAC database are used to construct specific binding site weight matrices for TFBS prediction. The user can inspect the result of the search through a graphical interface and downloadable text files. PROMO is using version 8.3 of TRANSFAC. Registration not required.

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Primer Blast logo
online PCR primer design
Subcategories: NCBI
Primer Blast allows: to design PCR primers

Primer Blast is a web application that uses Primer3 to design PCR primers and then submits them to BLAST search against user-selected database. The blast results are then automatically analyzed to avoid primer pairs that can cause amplification of targets other than the input template. Registration not required.

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DiRE logo
analysis of transcription factor binding sites
Subcategories: NCBI

DiRE (Distant Regulatory Elements of co-regulated genes) uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. Registration not required.

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Lasagna-Search logo

Lasagna search is an integrated user friendly web tool for transcription factor binding site search and visualization. Registration not required.

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iCODEHOP logo

The goal of iCODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primers) is to simplify the process of designing degenerate PCR primers by integrating both new and existing bioinformatics tools into an interactive, Open Source, Web application. This beta version of the new program is currently available to interested researchers for free. In addition to simplifying degenerate primer design workflows, iCODEHOP extends and improves the CODEHOP method of designing degenerate PCR primers from protein multiple alignments. iCODEHOP provides interactive visualization of PCR primers designed using the algorithm. Users can quickly scan over an entire set of degenerate primers produced by the program to assess their relative quality and select individual degenerate primers for further analysis. The program predicts annealing temperatures for degenerate primer pools, displays phylogenetic information for the sequences covered by the primer, and allows the user to easily design new degenerate primers from sub-selections of their input sequences. Registration not required.

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Graphpad Molarity Calculators logo

Molarity Calculators (QuickCalcs) is a web application (no installation required) that helps to dilute a stock solution or to calculate molarity from mass and volume, mass from volume and concentration, volume from mass and concentration. Registration not required.

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PCR Now logo
A Real-Time PCR Primer Design Tool

PCR Now permits to design Real-Time Polymerase Chain Reaction (RT-PCR) primers for any number of user-defined coding sequences. Great control over primer properties. Registration not required.

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rVista logo
high-throughput discovery of functional regulatory elements

Finding potential regulatory elements in noncoding regions of the human genome is a challenging problem. Analyzing novel sequences for the presence of known transcription factor binding sites or their weight matrices produces a huge number of false positive predictions that are randomly and uniformily distributed. rVista combines database searches with comparative sequence analysis, reducing the number of false positive predictions by ~95% while maintaining a high sensitivity of the search.

G. Loots and I. Ovcharenko, rVista 2.0: evolutionary analysis of transcription factor binding sites, Nucleic Acids Research, 32(Web Server Issue), W217-W221 (2004) Registration not required.

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OligoCalc logo
an online oligonucleotide properties calculator

OligoCalc is a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. OligoCalc has a familiar ‘calculator’ look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature. Since it first came online in 1997, there have been more than 900 000 accesses of OligoCalc from nearly 200 000 distinct hosts, excluding search engines

Citation: Kibbe WA. OligoCalc: an online oligonucleotide properties calculator, Nucleic Acids Res. 35(webserver issue): May 25, 007. Registration not required.

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Wikigenes logo

Wikigenes is the first wiki system to combine the collaborative and largely altruistic possibilities of wikis with explicit authorship. In view of the extraordinary success of Wikipedia there remains no doubt about the potential of collaborative publishing, yet its adoption in science has been limited." So writes Robert Hofmann of MIT in a Perspective article in the September edition of Nature Genetics (40, 1047-1051; 2008) about this "dynamic collaborative knowledge base for the life sciences that provides authors with due credit and that can evolve via continual revision and traditional peer review into a rigorous scientific tool. Registration not required.

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Normal Curve Generator logo

It's a simple and well constructed Excel spreadsheet from Jon Wittwer of Vertex42 for graphing a Normal distribution curve by inputing either a mean & SD or single subject values. In addition the spreadsheet includes examples for generating a random number from a Normal distribution, for calculating cumulative probabilities and for shading a portion of the distribution. Registration not required.

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Convert-me logo

Online conversions (e.g. metric conversions) for many measurement systems. Conversion tables are provided for both common (U.S., metric, etc.) and quite exotic units like Ancient Greek and Roman. You can also ask your questions and discuss how to convert units on our Units Conversion Forum. Registration not required.

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Ensembl logo
browsing genes and genomes

Ensembl, a genome browser project, produces genome databases for vertebrates, and makes this information freely available online. Registration not required.

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Primer3 Plus logo

Primer3 Plus is the new improved web interface to the popular Primer3 primer design program. Registration not required.

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