Bioinformatics Links Directory Features curated links to molecular resources, tools and databases. All of the resources are well tested and are either free or available for a nominal fee. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field. All links contained in the NAR Webserver issue since 2003 are also listed.

BIOVIEWS Java programs that show views of Drosophila Genome Project data at different levels of detail - from entire chromosome maps to nucleotide sequence data.

CINEMA A Colour INteractive Editor for Multiple Alignments program that allows visualization and manipulation of both protein and DNA sequences.

Dna Primer Melt Calculator A handy calculator of PCR primers. A nice justified layout of the sequence with codon numbering.

EMBOSS "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

EMBOSS Sequence Analysis Servers A suite of free software tools for sequence analysis, including that of GCG. There are a wide variety of programs that make up the suite, ranging in application from database searching to presentation of sequence data.

Flies In Your Java This is a map display of Drosophila genes, aberrations, clones and like items created with the new Java network programming language.

GCG: Genetics Computer Group It enables scientists to analyze DNA and protein sequences by editing, mapping, comparing, and aligning them. Other programs facilitate RNA secondary structure prediction, DNA fragment assembly, and evolutionary analysis. GCG serves molecular biologists by building practical tools that implement the most important techniques of mathematical biology.

JALVIEW A multiple alignment editor written entirely in Java. It was initially to be used as a visualization tool for the pFAM CORBA SERVER and client at the EBI but is available as a general purpose alignment editor.

JAMBW: Java-based Molecular Biology Workbench The programs and documentation have been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has.

JELLYFISH Simplifies and streamlines gene analysis with wide variety of functions including: graphic sequence display, one-click submission of sequences to BLAST and other analysis websites, drag-and-chop alignments, oligoanalysis, access to several internet based bioinformatics tools.

LabOnWeb Life science research engine. A collection of gene discovery tools designed to accelerate work in the lab, improve the quality and accuracy of experiments, simplify the delivery of information and help researchers make more informed decisions throughout the discovery process.

Match-Box Web Server Proposes protein sequence alignment tools based on strict statistical criteria. The method circumvents the gap penalty requirement. The Match-Box program is particularly suitable for finding and aligning conserved structural motives, in particular in protein core.

NCBI Tool Box for Software Developers at IEB The Information Engineering Branch (IEB) is responsible for designing and building NCBI's production software and databases.These resources constitute the bulk of what is seen on NCBI's Web pages. Meant primarily for software developers or other interested groups.

NCBI Tools for Software Developers The NCBI ToolBox consists of three major parts: Data Model - An explicit data model of biological sequences, structures, bibliographic data, and associated annotations. Data Encoding - A formal specification and encoding rules. Programming Libraries

PDB3D: Realtime 3D Molecule Renderer for the WWW A high speed 3D molecule rendering applet which has been designed specifically for viewing Protein Data Bank (PDB) forat molecular structure files within web pages.

Rasmol & Chime: Molecular Visualization Freeware RasMol is free software for looking at molecular structures. Chime shows molecules like RasMol, but unlike RasMol, Chime shows molecules inside a web page.

SEAVIEW A graphical multiple sequence alignment editor.

SHUFFLE This program, given a sequence of symbols, generates a new version of it consisting of the same symbols but in a randomized order.

Software Seek From Genomics.Com A repository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry.

Sstructview: RNA Secondary Structure Java Applet A reusable interface based on the standard two dimensional (2D) layout of RNA secondary structure.

The BioCatalog A software directory of general interest in molecular biology and genetics.

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