Genomics & DNA Sequence Analysis
Bioinformatics & Genomics
Companies, Publishers, & Books
Compendiums & Lists of Resource Links
Compounds & Enzymes
Educational & Information Resources
Genomics & DNA Sequence Analysis
DNA Sequence Analysis
DNA Sequencing Software
Genomic Search Servers
Hidden Markov Models
Major Sites & Organizations
Metabolic Pathway Databases & Related
Molecular Modeling & Visualization
Motif, Domain, Profile, Pattern, & Repeat Searches
Multiple Alignment & Phylogeny
Protein & Nucleic Acid Search Servers
Protein Analysis from Sequence
Sites with Multiple or Integrated Tools
Software Catalogues, Lists, & Downloads
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[ICGEBnet] Predicts DNA bendability and curvature from DNA sequences.
Crown Human Genome Center
[Weizmann Institute of Science] The Center deals with various aspects of the world wide Human Genome Project. Among its various activities, it offers consultation and practical help in gene mapping, database search, genomic clone identification, and genomic sequencing.
CUTG: Codon Usage Tabulated from GenBank
[National Institute of Genetics] Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.
DNA MFold Server
[Washington Univ. Medical School] DNA folding prediction by energy minimization.
[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.
[ISREC] This is a java applet that does Dot Plots (pairwise sequence comparisons). This site also contains examples with interpretations of Dot Plots, including protein repeat regions and intron and exon patterns in DNA.
[Science Magazine] Among the site’s offerings: 1) Links to breaking news in genomics and biotech, from Science, ScienceNOW, and selected other sources. 2) Pointers to classic papers, reviews, and new research, organized by categories relevant to the postgenomic world. 3) A page devoted to Science’s genome special issues. 4) Collections of web resources in genomics and postgenomics,including special pages on model organisms, educational resources, and genome maps. 5) A special node of news, information, and links on the biotech industry.
[Medical Research Council, UK] A program for the analysis of bacterial genomes.
[Weizmann Institute of Science ] GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
Compare the numerical order of protein-coding genes in two genomes, using GenBank genome files. Or compare a user-created list of protein sequences with a genome or another list. Program creates a dotplot of matches in proteins coded by genes, plotted in numerical order along the genome (or list). Points are plotted at different levels of significance for matching amino acid sequences. Program also generates a clickable list of matches. Genome size limited to less than 250 kb.
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[Gladstone Institutes, UCSF] GenMAPP is a free computer application designed to visualize gene
expression data on maps representing biological pathways and groupings
[Nature Journal] A comprehensive web resource devoted to genomics and with free access. The site includes a library of original research papers, a news service, applications of sequencing research and the technologies, and links to other genomics sites.
Large Dot Plots
[Virtual Genome Center] A fast dot plot algorithm designed for large DNA sequences to be compared with itself.
Mouse Genome Informatics
[The Jackson Laboratory] An index of research documenting data on endogeneous gene expression during mouse development that have been published from May 1993 to present.
[Murdoch University] The Online Researchers Bioinformatics Interface Tools project was established to implement an easy to use web based
interface for registered members of the Murdoch Bioinformatics Research
Group (MBRG). The system provides interfaces to the server side programs BLAST, Repeat Masker, and ClustalW; while still providing a framework for many other programs to be added to the interface in
the future. This is a downloaded Java program.
[EMBL] A tool for calculating of probable DNA level point mutations underlying known amino acid substitutions.
RNA Editing Web Site
[Univ. of California at Los Angeles] A site for the dissemination of information on all the various types of RNA editing.
[TIGR] A list of links to very useful molecular biology and bioinformatics-related freeware. The list includes programs for DNA sequencing and sequence analysis, genomic searches, and microarray image processing.
[ExPASy] A tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
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