Software
Bank cuts UK rates to 57-year low The Bank of England has cut interest rates by one percentage point from 3% to 2%, their lowest level since 1951. news.bbc.co.uk DNA dilemma Will European ruling result in more unsolved crimes? news.bbc.co.uk Interest rates Which lenders are passing on the rate cuts to customers? news.bbc.co.uk Pompey crash out after defeat Portsmouth exit the Uefa Cup after they lose to Bundesliga side Wolfsburg. news.bbc.co.uk HET will continue 'crucial work' The special police team set up to investigate murders during the troubles is to make 75 staff redundant. news.bbc.co.uk Carmakers 'affect entire US economy' General Motors boss Rick Wagoner and his Ford counterpart Alan Mulally admit making mistakes in the way they ran the firms. news.bbc.co.uk Menezes family's inquest protest The family of Jean Charles de Menezes have walked out of the inquest into his death at the Oval Cricket Ground in London in protest. news.bbc.co.uk Villa through despite Uefa Cup loss Aston Villa falll to a shock defeat to MSK Zilina but still reach the Uefa Cup's last 32, thanks to Hamburg's victory over Slavia Prague. news.bbc.co.uk Your pictures Readers' images of snowfalls across the UK news.bbc.co.uk Send your video, pictures and story ideas Have you got a good story? BBC News wants to hear from you. news.bbc.co.uk Smith accused of raid 'ignorance' Jacqui Smith is attacked for not knowing a Tory MP was to be arrested, as her predecessor says she should have been told. news.bbc.co.uk No decision over Shields pardon The High Court reserves judgement in the case of jailed Liverpool fan Michael Shields, who has started a pardon bid. news.bbc.co.uk Honda poised to quit Formula One Japanese car giant Honda will withdraw from Formula One on Friday and place its team up for sale, BBC Sport understands. news.bbc.co.uk Secondary school closures agreed A council agrees to close three secondary schools and create a new Welsh medium school as part of its reorganisation plans. news.bbc.co.uk Kenya PM calls for Mugabe removal Power-sharing in Zimbabwe is dead and Africa must unite to oust President Mugabe, says Kenya's prime minister. news.bbc.co.uk US Congresswoman hangs up on Obama A US Congresswoman hangs up the phone on President-elect Barack Obama, thinking the call is a hoax. news.bbc.co.uk Nasa delays its next Mars mission The US space agency (Nasa) has delayed the launch of its Mars Science Laboratory rover mission from 2009 to 2011. news.bbc.co.uk Mother guilty over Shannon kidnap Shannon Matthews's mother and co-accused Michael Donovan are convicted of kidnapping the nine-year-old in a plot to claim a £50,000 reward. news.bbc.co.uk Pakistan dilemma Relations with India strained in wake of the Mumbai attacks news.bbc.co.uk Child protection review announced The Scottish Government announces a wide-ranging review of guidance on child protection practices. news.bbc.co.uk Controversial Lapland theme park closes down The firm running a Lapland-style theme park in the New Forest criticised by visitors as "hell" and a "scam" close it down. news.bbc.co.uk Rhys killing 'appalled country' The murder of schoolboy Rhys Jones was a terrible killing which appalled the whole country, a judge tells a jury in his summing up. news.bbc.co.uk Nice smell... But why else would anyone buy a new car these days? news.bbc.co.uk Cash glow How much does a street light cost for one night? news.bbc.co.uk DNA database 'breached rights' Keeping the DNA of two Britons with no convictions was a breach of their human rights, a European court rules. news.bbc.co.uk | World Catalog > Science > Biology > Bioinformatics > Software Last searches:gameshsbcflight insuranceในหลวงkatrina kaifboat refinancing World Catalog > Science > Biology > Bioinformatics > SoftwareSoftware:Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML). http://adfconverter.sourceforge.net/ Text mining tool for genomics, proteomics platforms and drug discovery. http://www.timelogic.com/aks/index.html Free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence. http://bioinformatics.org/annhyb/ Free Classified Ads Portal www.graand.com Knoppix based bioinformatics software tools. Bootable from CD. http://opensource.nus.edu.sg/wiki/index.php/APBioKnoppix A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C. http://www.arb-home.de ARCiB -- Accessible Retired Computers in Biology NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms. http://arcib.dowling.edu/ Biochemfusion: Enabling Biochemformatics Software for working with post-translationally or chemically modified peptides and proteins including proteins as both sequences and chemical structures. http://www.biochemfusion.com Free Windows biological sequence alignment editor. http://www.mbio.ncsu.edu/BioEdit/bioedit.html Provides access to a number of tools including biological databases, sequence allignment, analysis and manipulation tools and structural analysis tools. Also provides a glossary of bioinformatics terms. http://www.bio32.com Bioinformatics Tools in Haskell A bioinformatics library implemented in Haskell, including various utilities based on it. http://malde.org/~ketil/ Biological Concept Diagram Editor A tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes. http://arrayanalysis.mbni.med.umich.edu/draw/ Workflow engine dedicated to bio-data synchronization and processing. http://biomaj.genouest.org Biomax BioXM Knowledge Management Environment Project-centered, distributed software platform that provides a central inventory of information and knowledge. Users create, manage and visualize scientific models as an extendible network of interrelated concepts. http://www.biomax.com/products/bioxm.php Commercial Mac OS X sequence analysis and structure visualization software. [PDF] http://www.lightwave-scientific.com/Resources/biOpen.pdf CentiBiN: Centralities in Biological Networks Application for the calculation and visualization of centralities for biological networks. http://centibin.ipk-gatersleben.de/ An interactive tool for peptide and nucleotide sequence analysis. http://cbrg.inf.ethz.ch/Darwin/index.html Small free Windows program to calculate nucleotides frequencies in DNA sequences. http://www.dnabaser.com/download/DNA-Counter/index.html Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X. http://www.lynnon.com A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. http://dnptrapper.sourceforge.net/ An open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics, machine-learning algorithms and visualization. http://www.ebi.ac.uk/expressionprofiler/ William Pearson's package for fast sequence comparison tools. http://www.ebi.ac.uk/Tools/fasta/ Free Windows tool for merging multiple FASTA files into a single FASTA file. http://www.dnabaser.com/download/FASTA-Converter/index.html An integrated multiple structure visualization and multiple sequence alignment application. Available for Windows, Linux. http://mozart.bio.neu.edu/friend/friend.html An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces. http://www.bioafrica.net/GDElinux/index.html This research software is designed for biologists and not computer scientists. It combines all the major DNA and protein sequence analysis tools into one software solution. http://www.geneious.com A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product. http://www.generunner.net Commercial Windows software for analyzing biochip image data. http://www.genespotter.de Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. http://sourceforge.net/projects/genome-tools/ Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English. http://gints.free.fr/english/eng_whatsAbout.htm GoCore is a free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner. http://www.helsinki.fi/project/ritvos/GoCore/ C-language implementations of generalized suffix-based algorithms useful for searching for string patterns in sets of input strings and is released under the terms of the LGPL license. http://compbio.charite.de/index.php/gsuffix.html Profiles protein sequence data using hidden Markov models of a statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. http://hmmer.janelia.org/ INCA - INteractive Codon Analysis Windows software that computes and charts codon and amino acid frequencies in whole genomes. Produces fully customizable scatter plots with the possibility to export graphics or text files for further analysis. Free for academic users. http://www.bioinfo-hr.org/inca Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. http://jaligner.sourceforge.net/ Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format. http://bioinf.dms.med.uniroma1.it/JSTRING/ Commercial graphical software for Blast searches. http://www.korilog.com/products/improving-NCBI-BLAST.php A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes. http://bioinf.wehi.edu.au/limmaGUI/index.html Multiple sequence alignment program for linux and other unix-like operating systems. Offers a range of multiple alignment strategies. http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ MaGe (Magnifying Genomes) - Microbial genome Annotation System The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes. http://www.genoscope.cns.fr/agc/mage/ MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH. http://www.cs.uni.edu/~okane/source/MARBL/proc1.html Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features. http://gel.ahabs.wisc.edu/mauve/ Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature. http://www.ariadnegenomics.com/products/medscan.html Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. http://www.ebi.ac.uk/~lenov/meltinghome.html Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego. http://metameme.sdsc.edu/ A sequence assembly suite with SNP detection for "hard" projects. http://chevreux.org/projects_mira.html Open source software developed by Timo Lassmann for multiple sequence alignment, including Kalign, Kalignvu and Mumsa. http://msa.cgb.ki.se/cgi-bin/msa.cgi Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays. http://nbc3.biologie.uni-kl.de BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. http://www.ncbi.nlm.nih.gov/BLAST/ NEXML: Phylogenetic Data in xml Exchange standard for representing phylogenetic data, inspired by the commonly used NEXUS format but more robust and easier to process. http://www.nexml.org Freeware DNA cloning, analysis and visualization software. http://www.acaclone.com DNA sequence assembler and finishing tools from the UW Genome Center. http://www.phrap.org/ A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commecial users. http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units. http://phylosort.sourceforge.net/ Developers of software for real time PCR primer design, TaqMan, molecular beacons, SYBR green, FRET, DNA microarray analysis, restriction cloning, plasmid maps, gateway cloning, protein interaction network and functional genomics. http://www.premierbiosoft.com/ Commercial software to analyses the red, green, blue, and gray color values of user-selected areas of images in gif, tiff, bmp, jpeg format. Windows 2000 and XP. http://www.immunokin.com Commercial Windows software for batch handling and analysis of nucleotide and protein sequences. http://www.seqtools.dk A freeware Java application that does many standard types of DNA and protein sequence analysis tasks. http://www.informagen.com/SA/ An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application. http://bioinformatics.org/sewer/ Predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. The web server version is free for academic use. http://sfold.wadsworth.org/index.pl 3D visualisation platform for Comparative Genomics visualisation. http://www.bcgsc.ca/gc/bomge/sockeye/ Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation. http://www.charite.de/bioinf/strap Search for Tandem Repeats IN Genomes. Includes C source code and examples. http://www.caspur.it/~castri/STRING/index.htm Software for simulating metabolic, signal and genetic networks. Home of SBW, Jarnac, JDesigner and winSCAMP. http://sbw.kgi.edu/ Locates and displays tandem repeats in DNA sequences. http://tandem.bu.edu/trf/trf.html Unipro UGENE: Integrated Bioinformatics Tools Free cross-platform bioinformatics software package for DNA and protein sequence analysis. http://ugene.unipro.ru The Washington University improved version of BLAST. Free for academic users. http://blast.wustl.edu/ A Linux/Unix visualization software system for evaluation of hybridisation experiments. http://www.molgen.mpg.de/~xdigitise/ | Send your video, pictures and story ideas Have you got a good story? BBC News wants to hear from you. news.bbc.co.uk Kenya PM calls for Mugabe removal Power-sharing in Zimbabwe is dead and Africa must unite to oust President Mugabe, says Kenya's prime minister. news.bbc.co.uk Cash glow How much does a street light cost for one night? news.bbc.co.uk DNA dilemma Will European ruling result in more unsolved crimes? news.bbc.co.uk Mother guilty over Shannon kidnap Shannon Matthews's mother and co-accused Michael Donovan are convicted of kidnapping the nine-year-old in a plot to claim a £50,000 reward. news.bbc.co.uk No decision over Shields pardon The High Court reserves judgement in the case of jailed Liverpool fan Michael Shields, who has started a pardon bid. news.bbc.co.uk Nasa delays its next Mars mission The US space agency (Nasa) has delayed the launch of its Mars Science Laboratory rover mission from 2009 to 2011. news.bbc.co.uk Pompey crash out after defeat Portsmouth exit the Uefa Cup after they lose to Bundesliga side Wolfsburg. news.bbc.co.uk Carmakers 'affect entire US economy' General Motors boss Rick Wagoner and his Ford counterpart Alan Mulally admit making mistakes in the way they ran the firms. news.bbc.co.uk US Congresswoman hangs up on Obama A US Congresswoman hangs up the phone on President-elect Barack Obama, thinking the call is a hoax. news.bbc.co.uk Nice smell... But why else would anyone buy a new car these days? news.bbc.co.uk HET will continue 'crucial work' The special police team set up to investigate murders during the troubles is to make 75 staff redundant. news.bbc.co.uk Pakistan dilemma Relations with India strained in wake of the Mumbai attacks news.bbc.co.uk Interest rates Which lenders are passing on the rate cuts to customers? news.bbc.co.uk Controversial Lapland theme park closes down The firm running a Lapland-style theme park in the New Forest criticised by visitors as "hell" and a "scam" close it down. news.bbc.co.uk Smith accused of raid 'ignorance' Jacqui Smith is attacked for not knowing a Tory MP was to be arrested, as her predecessor says she should have been told. news.bbc.co.uk Menezes family's inquest protest The family of Jean Charles de Menezes have walked out of the inquest into his death at the Oval Cricket Ground in London in protest. news.bbc.co.uk Rhys killing 'appalled country' The murder of schoolboy Rhys Jones was a terrible killing which appalled the whole country, a judge tells a jury in his summing up. news.bbc.co.uk Honda poised to quit Formula One Japanese car giant Honda will withdraw from Formula One on Friday and place its team up for sale, BBC Sport understands. news.bbc.co.uk Bank cuts UK rates to 57-year low The Bank of England has cut interest rates by one percentage point from 3% to 2%, their lowest level since 1951. news.bbc.co.uk Child protection review announced The Scottish Government announces a wide-ranging review of guidance on child protection practices. news.bbc.co.uk Villa through despite Uefa Cup loss Aston Villa falll to a shock defeat to MSK Zilina but still reach the Uefa Cup's last 32, thanks to Hamburg's victory over Slavia Prague. news.bbc.co.uk DNA database 'breached rights' Keeping the DNA of two Britons with no convictions was a breach of their human rights, a European court rules. news.bbc.co.uk Secondary school closures agreed A council agrees to close three secondary schools and create a new Welsh medium school as part of its reorganisation plans. news.bbc.co.uk Your pictures Readers' images of snowfalls across the UK news.bbc.co.uk |
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