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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
Biomedical search tools
Online genomic tools
Online proteomics tools
Calculators
Biomedical lab tools
Scientific writing/reading
Biomedical communities
Biomedical funding and jobs
Medical topics
Biomedical softwares