Bioinformatics programs included in DNALinux
ApE- A Plasmid Editor
in Windows (tested on 98, XP, NT), OS X(10.3, 10.4 and 10.5), and
Linux/Unix, highlights restriction sites in the editing window, shows
translation, Tm, %GC, ORF of selected DNA in real-time, reads DNA
Strider, Fasta, Genbank and EMBL files, copy and save graphics as
Windows metafiles (MS Windows only) in an other features. For more
information visit the web site.
Web site: http://www.biology.utah.edu/jorgensen/wayned/ape/
is a suite of automated docking tools. It is designed to predict how
small molecules, such as substrates or drug candidates, bind to a
receptor of known 3D structure. AutoDock actually consists of two main
programs: AutoDock performs the docking of the ligand to a set of grids
describing the target protein; AutoGrid pre-calculates these grids. In
addition to using them for docking, the atomic affinity grids can be
visualised. This can help, for example, to guide organic synthetic
chemists design better binders.
Web site: http://autodock.scripps.edu/
Morris GM, Goodsell DS, Huey R, Olson AJ. Distributed automated docking
of flexible ligands to proteins: parallel applications of AutoDock 2.4.
J Comput Aided Mol Des. 1996 Aug;10(4):293-304. Pubmed
a set of freely available tools for biological computation written in
Python by an international team of developers.
is a distributed collaborative effort to develop Python libraries and
applications which address the needs of current and future work in
bioinformatics. The source code is made available under the Biopython
License, which is extremely liberal and compatible with almost every
license in the world. We work along with the Open Bioinformatics
Foundation, who generously provide web and CVS space for the project.
Web site: www.biopython.org
Other documentation: Bassi S (2007) A Primer on Python for Life Science Researchers. PLoS Comput Biol 3(11): e199. doi:10.1371/journal.pcbi.0030199
Python for Bioinformatics
book by Sebastian Bassi
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I,
Hamelryck T, Kauff F, Wilczynski B, and de Hoon MJ. Biopython: freely
available Python tools for computational molecular biology and
bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3.
doi:10.1093/bioinformatics/btp163 pmid:19304878. Pubmed
Basic Local Alignment Search Tool (BLAST) finds regions of local
similarity between sequences. The program compares nucleotide or
protein sequences to sequence databases and calculates the statistical
significance of matches. BLAST can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.
Web site: http://blast.ncbi.nlm.nih.gov/
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui
Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped
BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Multiple alignment of nucleic acid and protein sequences.
X is a windows interface for the ClustalW multiple sequence alignment
program. It provides an integrated environment for performing multiple
sequence and profile alignments and analysing the results. The sequence
alignment is displayed in a window on the screen. A versatile coloring
scheme has been incorporated allowing you to highlight conserved
features in the alignment. The pull-down menus at the top of the window
allow you to select all the options required for traditional multiple
sequence and profile alignment.
Web site: http://www.clustal.org/
Jeanmougin,F., Thompson,J.D., Gouy,M., Higgins,D.G. and Gibson,T.J.
(1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci,
is "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.
Web site: www.emboss.org
Rice,P. Longden,I. and Bleasby,A. EMBOSS: The European Molecular
Biology Open Software Suite (2000) Trends in Genetics 16, (6)
displays a simple character-based menu that allows you to display the
names of emboss programs and select them. It also displays the names of
files in your current directory and allows you to display their
contents, copy them, delete them and do other things with them. emnu
allows to to move around the menus of programs or files using the arrow
keys. Pressing RETURN when you have selected an item will run a program
or display a file.
Web site: http://web.mit.edu/emboss_v4.0.0/www/embassy/emnu/emnu.html
Align an mRNA to a genomic DNA sequence
Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/esim4/esim4.html
L, Hartzell G, Zhang Z, Rubin GM, Miller W. "A computer program for
aligning a cDNA sequence with a genomic DNA sequence." Genome Res 1998
DNA sequence chromatogram trace viewer.
FinchTV utility for viewing chromatogram files is a stand-alone
application researchers use to easily view and edit their sequencing
data with dynamic interactivity.
Web site: http://www.geospiza.com/Products/finchtv.shtml
hidden Markov models (profile HMMs) can be used to do sensitive
database searching using statistical descriptions of a sequence
family's consensus. HMMER is a freely distributable implementation of
profile HMM software for protein sequence analysis.
Web site: http://hmmer.janelia.org/
The theory behind profile HMMs: R. Durbin, S. Eddy, A. Krogh, and G.
Mitchison, Biological sequence analysis: probabilistic models
proteins and nucleic acids, Cambridge University Press, 1998.
is a command line tool to perform multiple alignment of biological
sequences. It employs the Wu-Manber string-matching algorithm, to
improve both the accuracy and speed of the alignment. It uses global,
progressive alignment approach, enriched by employing an approximate
string-matching algorithm to calculate sequence distances and by
incorporating local matches into the otherwise global alignment. In
comparisons made by its authors, Kalign was about 10 times faster than
ClustalW and, depending on the alignment size, up to 50 times faster
than popular iterative methods.
Web site: http://msa.sbc.su.se/cgi-bin/msa.cgi
Timo Lassmann and Erik LL Sonnhammer. Kalign – an accurate and fast
multiple sequence alignment algorithm. BMC Bioinformatics 2005,
Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/memenew/ememe.html
mira genome fragment assembler is a specialised assembler for
sequencing projects classified as 'hard' due to high number of similar
repeats. For EST transcripts, miraEST is specialised on reconstructing
pristine mRNA transcripts while detecting and classifying single
nucleotide polymorphisms (SNP) occuring in different variations
The assembly system is using iterative multipass
strategies centered on usage of high confidence regions within
sequences and has a fallback strategy for using low confidence regions
Web site: http://chevreux.org/projects_mira.html
Multiple Sequence Editor
Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/mse/mse.html
provides a directory structure and makefile stubs for developing your
own applications more easily than in versions before 3.0.0.
Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/myemboss/
NCBI Toolkit is a collection of utilities developed for the production
and distribution of GenBank, Entrez, BLAST, and related services by the
National Center for Biotechnology Information. It includes the popular
bioinformatics tools formatdb and blastall.
Web site: http://www.ncbi.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML
(the PHYLogeny Inference Package) is a package of programs for
inferring phylogenies (evolutionary trees). It is available free over
the Internet, and written to work on as many different kinds of
computer systems as possible.
Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6.
Distributed by the author. Department of Genome Sciences, University of
Web site: http://evolution.gs.washington.edu/phylip.html
is a software suite for (bio)polymer mass spectrometry that is Free
Software developed on GNU/Linux. It allows the definition of polymer
chemistries and the simulation/analysis of mass spectrometric data
obtained on (bio)polymers.
Filippo Rusconi, GNU polyxmass: a software framework for mass
spectrometric simulations of linear (bio-)polymeric analytes. BMC
Bioinformatics 2006, 7:226doi:10.1186/1471-2105-7-226
Primer3 1.1.4 / Primer3plus
(Web GUI for primer3)
is a widely used program for designing PCR primers (PCR = "Polymerase
Chain Reaction"). PCR is an essential and ubiquitous tool in genetics
and molecular biology. Primer3 can also design hybridization probes and
Web site: http://primer3.sourceforge.net/
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and
for biologist programmers. In: Krawetz S, Misener S (eds)
Bioinformatics Methods and Protocols: Methods in Molecular Biology.
Humana Press, Totowa, NJ, pp 365-386
is an open-source, user-sponsored, molecular visualization system
created by Warren Lyford DeLano and commercialized by DeLano Scientific
LLC, which is a private software company dedicated to creating useful
tools that become universally accessible to scientific and educational
Web site: http://www.pymol.org/
RasMol is a molecular graphics program intended for the visualisation
of proteins, nucleic acids and small molecules.
Web site: http://www.rasmol.org/
Reads and writes nucleic/protein sequences in various formats. Data
files may have multiple sequences.
Sigma Align 1.1.1
tools for multiple-sequence alignment are focussed on aligning protein
sequence or protein-coding DNA sequence. Sigma ("Simple greedy multiple
alignment") is an alignment program with a new algorithm and scoring
scheme designed specifically for non-coding DNA sequence.
Web site: http://www.imsc.res.in/~rsidd/sigma/
Rahul Siddharthan, "Sigma: multiple alignment of weakly-conserved
non-coding DNA sequences", BMC Bioinformatics 7:143 (2006). Pubmed
Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/signature/
Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/structure/
computes phylogenetic trees from molecular sequences. The program
infers even large trees by maximum likelihood under a variety of models
of sequence evolution. It accepts both nucleotide and amino acid data
and takes rate heterogeneity into account. Separate models can be
assumed for user-defined data partitions, separate rates, separate edge
lengths, separate character compositions. All parameters can be
estimated from the data. Tree search can be guided by user-supplied
topological constraints and start trees.
Web site: http://www.treefinder.de/
Other documentation: Manual is available in pdf
Jobb, G., A. von Haeseler, and K. Strimmer. TREEFINDER: A powerful
graphical analysis environment for molecular phylogenetics. 2004. BMC
Evolutionary Biology. Pubmed
provides a simple way to view the contents of a NEXUS, PHYLIP,
Hennig86, Clustal, or other format tree file. While PAUP and MacClade
have excellent tree printing facilities, there may be times you just
want to view the trees without having to load the data set they were
generated from. The PHYLIP package contains tree drawing programs which
offer a greater variety of trees than TreeView, but are somewhat clumsy
to use. The forthcoming PAUP* for Windows does not have a graphical
interface, hence TreeView allows you to create publication quality
trees from PAUP files, either directly, or by generating graphics files
for editing by other programs.
Web site: http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic
trees on personal computers. Computer Applications in the Biosciences
TOPO creates an image of a transmembrane protein.
Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/topo/topo.html
Vienna RNA 1.8.25
Vienna RNA Package consists of a C code library and several stand-alone
programs for the prediction and comparison of RNA secondary structures.
secondary structure prediction through energy minimization is the most
used function in the package. We provide three kinds of dynamic
programming algorithms for structure prediction: the minimum free
energy algorithm of (Zuker & Stiegler 1981) which yields a
optimal structure, the partition function algorithm of (McCaskill 1990)
which calculates base pair probabilities in the thermodynamic ensemble,
and the suboptimal folding algorithm of (Wuchty et.al 1999) which
generates all suboptimal structures within a given energy range of the
optimal energy. For secondary structure comparison, the package
contains several measures of distance (dissimilarities) using either
string alignment or tree-editing (Shapiro & Zhang 1990).
we provide an algorithm to design sequences with a predefined structure
Web site: http://www.tbi.univie.ac.at/RNA/
Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian
Bonhoeffer, Manfred Tacker, and Peter Schuster. Fast Folding and
Comparison of RNA Secondary Structures. Appeared in: Monatsh.Chem. 125: