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NCBI BLAST - http://www.ncbi.nlm.nih.gov/BLAST/
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. |
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Phrap/Consed - http://www.phrap.org/
DNA sequence assembler and finishing tools from the UW Genome Center. |
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EMBOSS - http://emboss.sourceforge.net/
The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG. |
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WU-BLAST - http://blast.wustl.edu/
The Washington University improved version of BLAST. Free for academic users. |
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Expression Profiler - http://www.ebi.ac.uk/expressionprofiler/
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. |
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Sockeye - http://www.bcgsc.ca/gc/bomge/sockeye/
3D visualisation platform for Comparative Genomics visualisation. |
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STRAP - http://www.charite.de/bioinf/strap
Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation. |
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The ARB Project - http://www.arb-home.de
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. |
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SeWeR - http://bioinformatics.org/sewer/
An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application. |
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Tandem Repeats Finder - http://tandem.bu.edu/trf/trf.html
Locates and displays tandem repeats in DNA sequences. |
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Meta-MEME - http://metameme.sdsc.edu/
Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego. |
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Premier Biosoft International - http://www.premierbiosoft.com/
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. |
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ARCiB -- Accessible Retired Computers in Biology - http://arcib.dowling.edu/
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. |
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MELTING - http://www.ebi.ac.uk/~lenov/meltinghome.html
Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. |
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limmaGUI - http://bioinf.wehi.edu.au/limmaGUI/index.html
A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes. |
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Sfold - http://sfold.wadsworth.org/index.pl
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. |
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Genome-tools Web Interface - http://sourceforge.net/projects/genome-tools/
Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. |
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Friend - http://mozart.bio.neu.edu/friend/friend.html
An integrated multiple structure visualization and multiple sequence alignment application. Available for Windows, Linux. |
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GDE - http://www.bioafrica.net/GDElinux/index.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. |
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FASTA Converter - http://www.dnabaser.com/download/FASTA-Converter/index.html
Free Windows tool for merging multiple FASTA files into a single FASTA file. |
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Nano+Bio-Centre - http://nbc3.biologie.uni-kl.de
Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays. |
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DNA Counter - http://www.dnabaser.com/download/DNA-Counter/index.html
Small free Windows program to calculate nucleotides frequencies in DNA sequences. |
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PHRED - http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm
A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commecial users. |
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AlmaKnowledgeServer - http://www.timelogic.com/aks/index.html
Text mining tool for genomics, proteomics platforms and drug discovery. |
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AnnHyb - http://bioinformatics.org/annhyb/
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. |
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ADF MAGE-ML - http://adfconverter.sourceforge.net/
Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML). |
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DNPTrapper - http://dnptrapper.sourceforge.net/
A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. |
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RGBG Analyzer - http://www.immunokin.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. |
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JSTRING - http://bioinf.dms.med.uniroma1.it/JSTRING/
Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format. |
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KoriBlast - http://www.korilog.com/products/improving-NCBI-BLAST.php
Commercial graphical software for Blast searches. |