Tuesday, February 24, 2009

Open Source for Bioinformatics

Gene Designer - a brilliant software tools that allows one to combine building blocks such as regulatory DNA elements (promoters, ribosome-binding sites) with amino acid sequences, affinity & protease cleave tags and cloning features and codon optimize for any expression host.

CLC Free Workbench - allows basic sequence analysis such as open reading frame determination, restriction site analysis, translation from DNA/ RNA to proteins, alignments, and tree reconstruction in a single window format.

Geneious :-(Alexei Drummond Biomatters Ltd. Auckland, New Zealand) provides an automatically-updating library of genomic and genetic data; for organizing and visualizing data. It provides a fully integrated, visually-advanced toolset for: sequence alignment and phylogenetics; sequence analysis including BLAST; protein structure viewing, NCBI, EMBL, Pubmed auto-find & much more ...

Genome2D - is for the visualization of transcriptome and other customized data sets (visualizes a bacterial genome with all relevant information such as gene orientation, operon structure, transcriptional terminators or regulator binding sites) on linear chromosome maps constructed from annotated bacterial genome sequences. For a complete list of what this incredible program will do see here. Images and data tables from Genome2D can easily be exported for further use in other presentation programs. (Reference: Baerends, R.J.S.,et al. (2004) Genome Biology, 5: R37).

EMBOSS (European Molecular Biology Open Source Software Suite) can be downloaded from here.

PHIRE - this Visual Basic program performs an algorithmic string-based search on bacteriophage genome sequences, discovering and extracting blocks displaying sequence similarity, corresponding to conserved regulatory elements contained within these genomes in a systematic manner, without any prior experimental or predictive knowledge. (Reference: Lavigne, R. et al. 2004. PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatics 20: 629-635).

MB DNA Analysis (Oleg Simakov) - MB is a free multi-functional DNA/protein analysis program. It's main advantage is that it combines all of the most widely used features needed for an advanced molecular analysis of genomic/proteomic data. Features of MB include a fast restriction analysis algorithm (included plasmid / linear DNA drawing), promoter analysis, calculation of molecular weights and chemical properties of proteins, prediction of the secondary protein structures (after Chou-Fasman). Protein analysis also includes sequence translation and codon usage table calculation. Other features: hierarchical multiple sequence alignment tool (with a feature to compare secondary structure of proteins), phylogenetic tree building, dot plot, estimation of isoelectric point for proteins, primer design. A tool for the structural analysis of alpha helices is also included in the main package.

GenePalette allows genome sequence visualization and navigation. Users can download from NCBI’s GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites, etc. can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization.

UniPro DPview:- (UniPro Bioinformatics Group, Russia) - this is a tool for finding and analyzing matches between genomes. The user can examine the matches, selecting them directly on the dotplot matrix. This program also allows one to build local alignments with specified parameters (match cost, mismatch and gap penalties), using a modification of the classic Smith-Waterman algorithm. It is possible to find not only the best alignment score-wise, but also so-called "suboptimal" ones which have slightly lesser scores.

Artemis a DNA sequence viewer and annotation tool (Sanger Centre)

SEQtools is a program package for routine handling and analysis of DNA and protein sequences. The package includes general facilities for sequence and contig editing, restriction enzyme mapping, translation, and repeat identification.

DNA Club - DNA analysis software, features include remove vector sequence, find, find ORF, sequence editing, translate to protein sequence, protein sequence editing, RE Map, RE Map with translation, PCR primer selection, primer or probe evaluation etc.

ZCURVE - is a new highly accurate system for recognizing protein coding genes in bacterial and archaeal genomes based on the Z curve theory of DNA sequence (Reference: F.-B. Guo, H.-Y. Ou & C.-T. Zhang (2003). Nucleic Acids Res. 31: 1780-1789). I have experience some problems in downloading their E. coli genome sequence for analysis and have attached a new version.

DNA for Windows is a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects.

RNAdraw: is an integrated program for RNA secondary structure calculation and analysis by Ole Matzura & Anders Wennborg (1996) Computer Applications in the Biosciences (CABIOS) 12: 247-249

RNAstructure - RNA Secondary Structure Prediction and Analysis for Microsoft Windows. This program includes a secondary structure prediction algorithm, a sequence editor, an integrated drawing tool, the OligoWalk program, OligoScreen, Dynalign, and a partition function calculator. (Reference: D.H. Mathews (2005) Bioinformatics 21: 2246 - 2253.)

loopDloop is a tool for drawing RNA secondary structures in molecular biology.

Chromas will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create. N.B. only the older versions of the software are free.

FinchTV - Another useful tool for viewing and editing electropherograms.

G-language Genome Analysis Environment provides a greater variety of useful genome analysis tools compared to most existing analysis software packages, and is also easily pluggable. All of its tools are accessible as Perl modules. To get started download genome files from GenBank in *.gbk format (GenBank flat file format).

WinGene - Used to give the reverse complement a given sequence, translate the sequence in all reading frames and identify ORFs (Export polypeptides encoded by a given ORF into WinPep), perform a oligomer analysis (base composition and melting temperature), and perform a restriction analysis.

GeneDoc is a full featured multiple sequence alignment editor, analyzer and shading utility for Windows.

Ridom TraceEdit - displays chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. (Reference: J. Rothgänger et al. 2006. Bioinformatics 22: 493-494).

DNA Master - is "perhaps the world's greatest sequence editor" and analysis package. Find under "computer."

GeSTer (V. Nagaraja, Indian Institute of Science, Bangalore. India) - is extremely useful in locating stem-loop structures, including rho-independent terminators in annotated genomes. Since it does not run conveniently on Windows XP see how you can modify the *.gbk file so that it works.

RepeatAround - is designed to find “direct repeats”, “inverted repeats”, “mirror repeats” and “complementary repeats”, from 3 bp to 64 bp length, in circular genomes. It processes input files directly extracted from GenBank database and several genomes can be input simultaneously. The program provides visualisation of the repeats location in the genomic structure and the search for specific motifs is also possible. Outputs can be obtained in a spreadsheet containing information on the number and location of the repeats. The software also generates random circular genomes, for statistical evaluations or comparisons between observed and expected repeats distributions.
(Reference: A. Goios et al. 2006. Mitochondrion. 6: 218-224.)

Staden Package - consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin). The package was originally developed at the MRC-LMB in Cambridge. It is now open source (BSD licence) and is hosted on sourceforge.net.

Seqool - sequence analysis software designed primarily for searching biological signals in nucleic acid sequences. The sequence analysis program package provides several pattern recognition models, but it also includes the most common sequence analysis statistics, such as GC content, codon usage, etc.

GENtle - software package for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.

Plasmid graphics:

ApE Plasmid Editor (M. Wayne Davis, Univ. Utah, U.S.A.) highlights and draws graphic maps using feature annotations from GenBank and EMBL files; creates graphic restriction maps - linear or circular with features indicated and allows BLAST analyses along with a number of other useful features.

pDRAW32 DNA analysis software by AcaClone software (Kjeld Olesen). pDRAW lets you enter a DNA name and coordinates for genetic elements, such as genes, to be plotted on your DNA plots.

Plasmid Processor (Department of Biochemistry and Biotechnology, University of Kuopio, Finland) - is a simple tool for plasmid presentation for scientific and educational purposes. It features both circular and linear DNA, user defined restriction sites, genes and multiple cloning site. In addition you can manipulate plasmid by inserting and deleting fragments. Created drawings can be copied to clipboard or saved to disk for later use. Printing from within the program is also supported.

BVTech Plasmid - with this program you can draw circular or linear plasmid map with double strands or single strand. You can label the plasmid with genes and restriction sites in different colors, text, and styles.

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