Bioinformatics & Genomics
Genomics & DNA Sequence Analysis
DNA Sequence Analysis
Regulatory Site Finding
Repeat & Vector Masking
Sites with Multiple Tools
DNA Sequencing Software
Genomic Search Servers
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Arabiodopsis Information Resource
[NCGR and the Carnegie Institution] TAIR provides literature and genomic data about the plant Arabidopsis thaliana .
Artemis sequence viewer
[The Sanger Centre, U. K.] The Artemis sequence viewer and annotation tool allows visualization of DNA sequence features and sequence analysis, including six-frame translation. Artemis can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Written in Java, Artemis is available for UNIX, Macintosh or MS Windows.
BCM Search Launcher: Pairwise Sequence Alignment
[Baylor College of Medicine] A site with multiple tools to align pairs of input sequences.
[ICGEBnet] Predicts DNA bendability and curvature from DNA sequences.
[Pasteur Institute] This program is able to determine a codon usage table, a distance matrix, and the values of base composition for a set of protein coding genes.
DARWIN Molecular Sequence Analysis
[CBRG] An interactive tool for peptide and nucleotide sequence analysis with a library of functions for sequence management and analysis, statistics, numerics, and graphics.
Deinococcus radiodurans Genome Search
[TIGR] Users can view the predicted coding regions found within a span of the Deinococcus radiodurans chromosome.
[National Cancer Institute] This software is for information analysis of protein and nucleic-acid sequences.
DNA Mutation Checker
[EMBL] A tool to verify the transcription and translation effects of DNA level sequence variation.
[UK HGMP Resource Center] A collection of DNA repeat-finding sites.
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[DNAssist] A DNA sequence editing and analysis application.
[Carlsberg Laboratory] Software for handling and analysis of nucleotide and protein sequences.
This downloadable package also has special functions for EST and SAGE handling and analysis.
[Karolinska Institutet, Center for Genomics Research] Compares two related sequences and finds matches, creating a dotplot. Accompanying the dotplot are excellent statistics and user-friendly adjustment of thresholds. Download the program to run on Unix. A server version is available at http://www.hgmp.mrc.ac.uk/Registered/Option/dotter.html for registered users.
[National Center for Biotechnology Information] PCR-based sequence tagged sites (STSs) have been used as landmarks for construction of various types of genomic maps. Using "electronic PCR" (e-PCR), these sites can be detected in DNA sequences, potentially allowing their map locations to be determined.
[Compugen] An algorithm for searching protein databases with DNA queries, based on Smith-Waterman. FramePlus independently and simultaneously models frame shifts and codon gaps.
[GenPak Inc.] Compare whole genomes at the DNA sequence level, looking for identical stretches of bases. Program creates a dotplot, sequence list, and statistics. Download a working version free, or pay for the expensive version.
[J. Ryan, NHGRI] Runs GRAIL, MZEF, GENSCAN, FGENES, Sputnik, RepeatMasker, and BLAST; and prints the output in ASN.1 format.
[EBI] Provides a highly automated analysis of biological sequences.
[CuraGen] This commercial sites offers a fully integrated genomics suite of
services, including discovery-oriented software for SeqCalling with sequence and SNP data, GeneCalling with gene expression data, PathCalling with protein -protein interactions and pathways, a pharmacogenomics database of drug profiles, and SNPCalling with our database of 200,000 cSNPs (gene-based single nucleotide polymorphisms).
[GSF] This software tool detects distance associations between sequence elements.
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MatInd and MatInspector2.1
[GSF] Tools for detection of consensus matches in nucleotide sequence data .
The Microbiology Network
Molecular Biology and Biotechnology File Archive.
These files include standard shareware
programs of interest to the microbiologist,
programs designed by individual investigators,
text files in specialized interest, and
demonstration programs supplied by vendors.
[Medical Research Council, UK] A program which takes a DNA sequence and determines how many single point mutations would result in nonsense, missense, or neutral mutations.
Nucleic Acid Structure Analysis
[International Union of Crystallography] This program calculates all of the rotational and translational parameters for complementary base pairs, neighboring base pairs in Cartesian and helical coordinate frames, and base to base Cartesian and helical parameters along each strand.
PCR primer selection
[Virtual Genome Center] Designed for selection of PCR primers to amplify regions from relatively low complexity genomes.
pDRAW32 DNA analysis software
[AcaClone Software] A free, feature-rich, DNA software application. Capabilities include annotation, cloning, sequence editing, enzyme selection, graphical output, and more. According to the author, "Actually pDRAW32 is not freeware - rather it is "beerware." This means that if you like the program you are encouraged to buy me a beer if you should meet me at a scientific meeting. You are mostly at risk of that if you attend conferences on yeast genetics."
Plant Genome Data & Information Center
[USDA National Agricultural Library] This USDA site provides access to a variety of information products and services that relate to many aspects of plant and animal biotechnology and genomics.
[consortium of several research laboratories] This genomics site is oriented to plant functional genomics. The site maintains servers for analyzing protein sequence, searching for patterns, and plotting motifs. The site also discusses plant protein phosphorylation.
[ICGEBnet] Plots various physiochemical, statistical, or locally computed parameters along DNA sequences (1-D or sequence-plots) or against each other (2-D plots).
[Whitehead Institute/MIT] Selects PCR primers from nucleotide sequences.
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[The Hospital for Sick Children, Toronto] (Alex Dong Li) Searches for DNA or protein sequence repeats.
Restriction Map Alignment
[USC Computational Biology] This program reads restriction maps and deciphers alignments using a quantic map alignment algorithm.
scan for matches
[Bioweb Pasteur] Search tool to search a protein or nucleic acid sequence for patterns. User may enter sequence or datafile to be searched, and sequence of pattern searched for.
[NCBI] A software package expressly designed for large-scale research projects in bioinformatics. Its goal is "to facilitate large-scale semi-automatic sequence analysis projects, leveraging human intelligence by simplifying laborious tasks, without taking human judgment out of the loop."
[Indiana Univ.] A biosequence sequence editor and analysis program for multiple sequence alignments and single sequence editing.
Sequence Manipulation Site
The Sequence Manipulation Suite is a collection of web-based
programs for analyzing and formatting DNA and protein sequences. The output of each program is a set of HTML commands, which is
rendered by your web browser as a standard web page. You can print
and save the results, and you can edit them using an HTML editor or a
[Australian National Univ.] This program estimates the amount of local sequence repetition in nucleotide sequences.
[Virtual Genome Center] Calculates the stability and predicts the temperature-dependent behavior of any DNA duplex structure from knowledge of its base sequence.
[NCBI] UniGene is an experimental systerm for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location. Additionally, expressed sequence tag (EST) sequences have been included.
Virtual Genome Center
An online resource for accessing tools and databases for Molecular Biologists.
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Web Primer: DNA and Purpose Entry
[SGD] A tool for DNA and purpose entry providing information on PCR and sequencing.
[First Market Research] (Max Heimann) A restriction enzyme mapping and analysis tool for a DNA sequence.
Yeast Genome Restriction Analysis
[SGD] Allows one to perform a restriction analysis by entering a sequence name or an arbitrary DNA sequence.