Bioinformatics Links Directory : Utilities

These resources are free, publicly available, multi-purpose tools for DNA sequence analysis. Links to resources for sequence presentation, manipulation tasks, and format conversion are found here.

BCM Search Launcher - (Found June 24, 2008 )

Molecular biology-related search and analysis services organized by function; single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters).
http://searchlauncher.bcm.tmc.edu/

Software for MacOSX at Mek&Tosj.com - (Found June 24, 2008 )

Freely available programs that run on the MacOSX platform. 4Peaks is a DNA sequence editor and visualization program able to read and write common trace file formats. iRNAi assists in the design of error-free oligos. EnzymeX is a tool to help determine which restriction enzymes to use and includes information for over 580 enzymes. LabAssistant is a tasktime management system to help organize your experiments.
http://www.mekentosj.com/programs/index.html

SeWeR - (Found June 24, 2008 )

Sequence analysis tools on the web; includes nucleic acid, protein, PCR and alignment tools.
http://bioinformatics.org/sewer/

PlasMapper - (Found June 24, 2008 )

Web server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.); allows users to define custom features to display; contains a library of commonly used plasmids; and, generates nice looking images in a variety of output formats.
http://wishart.biology.ualberta.ca/PlasMapper/index.html

pDRAW32 - (Found June 24, 2008 )

pDRAW32 is a multi-function tool with features including: graphical displays useful for drawing plasmids, sequence analysis and editing, virtual agarose gel plots and homology plots.
http://www.acaclone.com/

OSU Bioinformatics and Computational Biology - (Found June 24, 2008 )

The website of the Ohio State University Human Cancer Genetics Bioinformatics group. This site has many resources, including databases of promoters and transcription factors, software tools to predict potential P53 consensus binding sites and to predict first exon and promoter regions and a software toolkit for developing web-based applications to view genomic data.
http://bioinformatics.med.ohio-state.edu/

DNAtools - (Found June 24, 2008 )

DNAtools include predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database.
http://hydra.icgeb.trieste.it/~kristian/dna/

Chinook - (Found June 24, 2008 )

Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application.
http://www.bcgsc.bc.ca/chinook/

Bioinformatics Toolkit - (Found June 24, 2008 )

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.
http://protevo.eb.tuebingen.mpg.de/toolkit/index.php?view=search

BCM Search Launcher Sequence Utilities - (Found June 24, 2008 )

Includes reverse complement, 6-frame translation, RepeatMasker, ReadSeq format conversion.
http://searchlauncher.bcm.tmc.edu/seq-util/seq-util.html