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Plasmid Map Templates
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    Research Abstract
  • Acta Laser Biology Sinica, 2007-5
  • Acta Laser Biology Sinica, 2007-4
  • Acta Laser Biology Sinica, 2007-3
  • Acta Laser Biology Sinica, 2007-2
  • Acta Laser Biology Sinica, 2007-1
  • Acta Laser Biology Sinica, 2006-6
  • Acta Laser Biology Sinica, 2006-5
  • Acta Laser Biology Sinica, 2006-4
  • Acta Laser Biology Sinica, 2006-3
  • Acta Laser Biology Sinica, 2006-2
  • Acta Laser Biology Sinica, 2006-1(Addition)
  • Acta Laser Biology Sinica, 2006-1
  • Acta Laser Biology Sinica, 2005-6
  • Acta Laser Biology Sinica, 2005-5

  • Bioinformatics Tools

    • ARTS - ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.
    • BLAST - Basic Local Alignment Search Tool; retrieve sequences similar to your query.
    • BankIt - Web-based submission of one or a few sequences to GenBank.
    • Cancer Genome Anatomy Project - Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.
    • dbSNP - Repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms; NCBI collaboration with NHGRI.
    • EBI Tools - EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services EBI provides through Simple Object Access Protocol (SOAP) and other related web service technologies.
    • Electronic PCR - Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.
    • EMBOSS - Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.
    • Entrez - NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.
    • FeatureExtract - The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.
    • Genelynx - A portal to the human genome. Query by text or BLAST, to access heaps of info from primary and secondary databases of genomic resources, transcripts, protein sequences, function, associated diseases, homologs, ests.
    • GtRDB - GtRDB: The Genomic tRNA Database Automated tRNA identifications by the program tRNAscan-SE on complete or nearly complete genomes.
    • MicroInspector - MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.
    • miRU - miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes.
    • Non-Coding RNA database - Non-translatable RNA transcripts that appear to work at the RNA level.
    • International HapMap Project - The haplotype map, or HapMap, is a tool that will allow researchers to find genes and genetic variations that affect health and disease.
    • Oligodb - Oligodb generates oligos suitable for expression experiments based on predicted gene transcripts from the Ensembl project. One can search for transcripts via keyword, or do a batch search by providing a list of Ensembl identifiers.
    • OligoWiz - OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript. .
    • Sequin - Desktop tool developed by the NCBI for editing, annotating and submitting DNA sequences to any of the three DNA sequence submission sites (DDBJ, EMBL or GenBank).
    • MartView - The Ensembl EnsMart Genome Browser (MartView) is a tool for data retrieval and data mining that integrates data from Ensembl. Through the web interface MartView allows you to apply a series of filters to create custom datasets which can be converted to several useful output formats.
    • MRS - MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.
    • Primer3 - Comprehensive PCR primer and hybridization probe design tool; many options but easy to accept defaults at first.
    • Riboswitch finder - RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.
    • RNAbase - RNAbase is a searchable and annotated database of all publicly available RNA structures.
    • SOURCE - Stanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat.
    • SRS - Sequence Retrieval System network browser for multiple molecular databases
    • WEBIN - WEBIN is the internet tool for the submission of nucleotide sequences to the EMBL database. It is a service offered by the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory.
    • WU BLAST - Washington University Basic Local Alignment Search Tool.
    • 3D-pssm - Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.
    • AISMIG - AISMIG (An Interactive Server-side Molecule Image Generator) is a tool for generating and visualizing high resolution 3D images from PDB structure files.
    • AS2TS - The AS2TS (Amino acid Sequence to Tertiary Structure) system consists of servers for protein structure analysis and modelling.
    • BhairPred - BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.
    • BioInfo3D - BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.
    • Bioverse - Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.
    • BSDD - BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.
    • CD-Search - CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.
    • Cn3D - Web browser helper application that simultaneously displays 3-D structure, sequence, and alignment.
    • ConSeq - ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue.
    • ElNemo - ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.
    • DeNovoID - DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.
    • ExPASy Proteomics tools - Various tools for protein identification and characterization, similarity searches, pattern and profile searches, post-translational modification prediction, and more.
    • GELBANK - GELBANK is a database of 2D gel images of proteomes for species with completed genomes. The user can search by sequence description or fragment, or by gel characteristics. Links are made between the sequence and gel when available.
    • GoMiner - GoMiner organizes and allows the visualization of large sets of genes based on Gene Ontology classifications.
    • Human Protein Reference Database - The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is curated by experts, who manually extract it from published literature.
    • MINER - MINER is a tool for the identification and visualization of phylogenetic motifs (regions within a multiple sequence alignment (MSA) that conserve the overall phylogeny of the complete family).
    • MMDB - Molecular Modelling Database of 3-D structures; experimentally determined structures only.
    • MolMovDB - The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.
    • MONSTER - MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.
    • PDB - Protein Data Bank; includes theoretical structures.
    • PDB2PQR Server - Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.
    • ProteinDBS - ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web.
    • RasMol - 3-D structure viewer, web browser helper application.
    • SPACE - SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes.
    • STRAP - The Structural Alignment Program for Proteins (STRAP) is a java-based program that can be run over the web using a Java Web Start enabled browser or downloaded and run as a stand-alone application. Alignments can be done using one of several methods, including ClustalW, JAligner and T_coffee. STRAP is also able to incorporate structure information and interfaces with programs such as Pymol and Rasmol. There is also a tutorial included.
    • Swiss-Prot and TrEMBL - Swiss-Prot is a curated database of protein sequences that are highly annotated and have a minimal level of redundancy. TrEMBL is a supplement to Swiss-Prot, containing computer-annotated translations of EMBL sequences.

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