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
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).
BCM Search Launcher Sequence Utilities
Includes reverse complement, 6-frame translation, RepeatMasker, ReadSeq format conversion.
Bioinformatics Toolkit
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.
BoxShade
Printing and shading of multiple alignment files.
DNAtools
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.
eBioinformatics
This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.
EMBOSS
Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.
HGNC: HUGO Gene Nomenclature Committee
The HGNC approves a unique gene name and symbol for each known human gene. The Human Gene Nomenclature Database (Genew) is searchable, and contains all approved symbols. For each symbol, if known, the database associates gene location, aliases, previous symbols and links out to sequence data.
NDB
NDB (Nucleic Acid Database) is a repository of three-dimensional structural information about nucleic acids.
OSU Bioinformatics and Computational Biology
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.
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.
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.
ReadSeq
Sequence format conversion; includes GenBank, EMBL, GCG, FASTA, ASN.1, Phylip and others.
SeWeR
Sequence analysis tools on the web; includes nucleic acid, protein, PCR and alignment tools.
Software for MacOSX at Mek&Tosj.com
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 task/time management system to help organize your experiments.
The Sequence Manipulation Suite 2
The Sequence Manipulation Suite is a set of tools for tasks such as sequence format conversion, sequence presentation, analysing sequence characteristics and shuffling or generating random sequences. It can be accessed over the web, or installed locally and run through a web browser.
VisCoSe (Visualization and Comparison of consensus Sequences) is a web based tool that takes a set of sequences (aligned or unaligned) and calculates a consensus sequence and the conservation rates for the sequence alignment, producing an easy to interpret visualization as output. One can also compare and visualize a set of consensus sequences generated from several sequence sets.
The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.
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