Bioinformatics programs included in DNALinux



ApE- A Plasmid Editor
Runs 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/

Other documentation:

Citation:




AutodockSuite 4.0.1

AutoDock 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/

Other documentation:

Citation: 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





Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
It 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

Citation: 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




Blast 2.2.20

The 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/

Other documentation:

Citation: 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.




ClustalX

Multiple alignment of nucleic acid and protein sequences.
Clustal 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/

Other documentation:

Citation: Jeanmougin,F., Thompson,J.D., Gouy,M., Higgins,D.G. and Gibson,T.J. (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci, 23, 403-5.





EMBOSS 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

Other documentation:

Citation: Rice,P. Longden,I. and Bleasby,A. EMBOSS: The European Molecular Biology Open Software Suite (2000) Trends in Genetics 16, (6) pp276--277.




EMNU-1.05
emnu 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

Other documentation:

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ESIM4-1.0.0
Align an mRNA to a genomic DNA sequence

Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/esim4/esim4.html

Other documentation:

Citation: Florea 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 Sep;8(9):967-74





FinchTV - DNA sequence chromatogram trace viewer.
The 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

Other documentation:

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HMMER-2.3.2
Profile 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/

Other documentation:

Citation: The theory behind profile HMMs: R. Durbin, S. Eddy, A. Krogh, and G. Mitchison,  Biological sequence analysis: probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998.



IPRSCAN-4.3.1
Web site:

Other documentation:

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Kalign 2.03
Kalign 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

Other documentation:

Citation: Timo Lassmann and Erik LL Sonnhammer. Kalign – an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 2005, 6:298doi:10.1186/1471-2105-6-298




MEMENEW-0.1.0
Motif detection

Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/memenew/ememe.html

Other documentation:

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MIRA-2.8.2
The 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 thereof.
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 when needed.

Web site: http://chevreux.org/projects_mira.html

Other documentation:

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MSE-1.0.0
Multiple Sequence Editor

Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/mse/mse.html

Other documentation:

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MYEMBOSS-6.0.0
MYEMBOSS 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/

Other documentation:

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NCBI Toolkit

The 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

Other documentation:

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PHYLIP (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 Washington, Seattle.

Web site: http://evolution.gs.washington.edu/phylip.html

Other documentation:

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Polyxmass 0.9.7
polyxmass 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.

Web site:

Other documentation:

Citation: 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)
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 sequencing primers.

Web site: http://primer3.sourceforge.net/

Other documentation:

Citation: 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




Pymol 1.0r2
PyMOL 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 communities.

Web site: http://www.pymol.org/

Other documentation:

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Rasmol 2.7.3.1
RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules.

Web site: http://www.rasmol.org/

Other documentation:

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readseq 1.7
Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.

Web site:

Other documentation:

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Sigma Align 1.1.1
Most 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/

Other documentation:

Citation: Rahul Siddharthan, "Sigma: multiple alignment of weakly-conserved non-coding DNA sequences", BMC Bioinformatics 7:143 (2006). Pubmed




SIGNATURE-0.1.0

Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/signature/

Other documentation:

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STRUCTURE-0.1.0

Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/structure/

Other documentation:

Citation:




 
TREEFINDER 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 format.

Citation: Jobb, G., A. von Haeseler, and K. Strimmer. TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics. 2004. BMC Evolutionary Biology. Pubmed




TreeView 0.5.1
TreeView 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

Other documentation:

Citation: Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.




TOPO-1.0.0
TOPO creates an image of a transmembrane protein.

Web site: http://saf.bio.caltech.edu/hhmi_manuals/solaris/embassy_apps/topo/topo.html

Other documentation:

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Vienna RNA 1.8.25

The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
RNA 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 single 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). Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding).

Web site: http://www.tbi.univie.ac.at/RNA/

Other documentation:

Citation: 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: 167-188 (1994).





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