Geneious Prime is a powerful bioinformatics software solution packed with fundamental molecular biology and sequence analysis tools. Perform a wide-range of cloning and primer design operations within one interface. Take charge with industry-leading assembly and mapping algorithms, and superior visualizations. Program for faster alignment of short oligonucleotides onto reference sequences for next generation sequencing data analysis. Sequence Manipulation Suite: JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. Superlink: Genetic linkage analysis with input-output relationships similar to those in standard. There are many applications for opening DNA sequence files on the PC, but few exist for opening them on the Mac. Furthermore, none of the existing software will generate quality reports for your DNA sequence chromatograms. To use this DNA sequence analysis software, simply drag and drop chromatogram files onto the program's icon. Artemis: a DNA sequence viewer and annotation tool (Sanger Centre) SEQtools is a program package for routine handling and analysis of DNA and protein sequences. The package includes general facilities for sequence and contig editing, restriction enzyme mapping, translation, and repeat identification. Free for students. The free Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers. CodonCode Aligner 5.1.5 a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X.
ONLINE ANALYSIS TOOLS
(INTERNET RESOURCES for MOLECULAR BIOLOGISTS)
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Analysis of nucleotide and protein sequence data was initially restricted to those with access to complicated mainframe or expensive desktop computer programs (for example PC/GENE, Lasergene, MacVector, Accelrys etc.). The availability of online tools permits even the novice molecular biologist the opportunity to derive a considerable amount of useful nformation from nucleotide or protein sequence data. For those with no experience I have provided three sequences: (a) a DNA sequence, (b) a protein sequence, and (c) four protein sequences presented in FASTA format. Prior to trying out a Web Site select the sequence and copy to clipboard. Each of the items in blue text is hyperlinked to a site on the Web. Each of these Web Sites has a box into which you can 'Paste' your sequence. Click on the button labeled 'Search,' 'Run' or 'Submit.' If in doubt use the default setting that the sites provide, but for the more adventuresome some of the sites offer the chance of modifying the search strategy.
ONLINE RESOURCES(tutorials and glossaries) - Needs work
TERTIARY STRUCTURE PREDICTIONS OF SACCHARIDES
ALIGNMENTS
CONVERT SEQUENCE(upper to low case, complement, reverse, RNA to DNA)
COMPOSITION
DNA MOTIFS
HOMOLOGY SEARCHES
MELTING TEMPERATURE (Tm)
PCR PRIMER DESIGN
PHYLOGENY
PROMOTERS
REPEATS & SECONDARY STRUCTURE
RESTRICTION ENDONUCLEASE SITES
TRANSLATION (GENERAL)
TRANSLATION (EUKARYOTIC GENES) (identification of introns and exons)
TRANSCRIPTION FACTORS
TOOLS FOR WHOLE GENOME ANALYSIS
ALIGNMENTS
COMPOSITION & CHEMISTRY
HOMOLOGY SEARCHES
MOTIFS
PHYLOGENY
QUATERNARY STRUCTURE PREDICTIONS
SECONDARY STRUCTURE PREDICTIONS
TERTIARY STRUCTURE PREDICTIONS
RNA ANALYSIS
PROMOTERS & TERMINATORS
TRANSCRIPTION FACTORS
BUFFERS
CENTRIFUGATION CALCULATIONS
GENERAL MOLECULAR BIOLOGY CALCULATIONS
META SITES FOR DNA & PROTEIN ANALYSIS
SEQUENCE CLEANUP & CONVERSION
ONLINE GRAPHICS
WINDOWS- & JAVA or PERL-BASED PROGRAMS- free molecular biology programs
DOWNLOADING SEQUENCES FROM GENBANK & MANIPULATING THEM IN BIOEDIT
The Bio-Web: Resources for Molecular and Cell Biologists is a non-commercial, educational site with the only purpose of facilitating access to biology-related information over the internet.
CREATED BY:Dr. Andrew M. Kropinski,Departments ofFood Science; and, Pathobiology University of Guelph,Guelph, Ontario, N1G 2W1 CANADA
Problems and suggestions: Contact - Andrew M. Kropinski (Email: Phage.Canada (at) gmail.com)
