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BLAST nucleotide (BLASTN) searches nucleotide subjects using a nucleotide query. Registration not required.
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Tfsitescan is intended for promoter sequence analysis and works best with sequences of ~500 nt Registration not required.
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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 (from Max Planck Isntitute of Molecular genetics) 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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PROMO (from Universitat Politècnica de Catalunya) from 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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a free database accessing the MEDLINE database of citations, abstracts and some full text articles on life sciences and biomedical topics
Category: Literature search
Pubmed allows: to search in the literature
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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analysis of transcription factor binding sites
Category: Transcription factors analysis
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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online PCR primer design
Category: PCR primers design
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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Lasagna search is an integrated user friendly web tool for transcription factor binding site search and visualization. Registration not required.
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Category: Calculators and converters
GraphPad Molarity Calculators allows: Calculate how to dilute a stock solution, calculate molarity from mass and volume, calculate mass from volume and concentration, calculate volume from mass and concentration
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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Multiple Sequence Alignment is the arrangement of several protein or nucleic acid sequences with postulated gaps so that similar residues (in one-letter code) are juxtaposed. Registration not required.
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high-throughput discovery of functional regulatory elements
Category: Transcription factors analysis
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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free online tool free plagiarism detection
Category: Plagiarism Detection
Dupli Checker allows: check for plagiarism
Dupli Checker is one of the most effective free plagiarism detection tools on the Internet. While it doesn’t have a fancy interface, it certainly gets the job done well. You don’t have to pay anything. Whether you are a one-time user or plan to make the most of this free plagiarism detection tool on a daily basis, you are not required to pay for subscription. You are presented with a very basic, functional layout that does not require for any previous experience with plagiarism detection tools. Duplichecker enables you to either copy and paste your text in the field and then check it for plagiarisms, or upload a Docx or Text file from your computer. If you sign up for free, Duplichecker allows you to do 50 plagiarism checks in a single day. If you choose not to indulge in a free sign-up then you are limited to only 1 plagiarism check per day. Registration not required.
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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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ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. The online version is hosted by EMBL. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Registration not required.
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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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Primer3 Plus is the new improved web interface to the popular Primer3 primer design program. Registration not required.
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PASTAA is a web app to evaluate if there is a regulatory association between transcription factors and groups of genes. Input: List of gene IDs. Registration not required.
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Naturejobs is in association with Nature magazine. It is a worldwide career resource for scientists, providing a wide range of career advice and information. Registration not required.
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Category: Calculators and converters
Mole/Gram Converters allows: convert between moles and grams, GraphPad
Biomedical search tools
Online genomic tools
Online proteomics tools
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Scientific writing/reading
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