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| emboss | 2.8.0 | GPL/LGPL | The European Molecular Biology Open Software Suite | EMBOSS is a new, 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. Reference for EMBOSS: Rice,P. Longden,I. and Bleasby,A. "EMBOSS: The European Molecular Biology Open Software Suite" Trends in Genetics June 2000, vol 16, No 6. pp.276-277 |
| freedelta | 0.20.1 | GPL | C++ classes for manipulating DELTA files | The Free DELTA project was launched in April, 2000 with the aim of creating a complete Linux-compatible free, legally unencumbered -- that is, not covered by any patents -- software system for processing taxonomic descriptions coded in DELTA format, following the decision by CSIRO Division of Entomology to stop funding the development of the original DELTA programs. |
| gibbs | 9.95 | Public Domain | Gibbs motif sampler | Gibbs motif sampler developed by A. Neuwald at the NCBI References for Gibbs: Neuwald, Liu, & Lawrence (1995) "Gibbs motif sampling: detection of bacterial outer membrane protein repeats" Protein Science 4, 1618-1632. Lawrence, Altschul, Boguski, Liu, Neuwald & Wootton (1993) "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment" Science 262:208-214. |
| ncbi-tools | 6.1 | Public Domain | NCBI tools | Tools from the NCBI toolkit. |
| primer3 | 0.9 | BSD like | PCR reactions primers identification | Primer3 is a complete rewrite of the original PRIMER program (Primer 0.5), written by Steve Lincoln, Mark Daly, and Eric Lander. Primer3 picks primers for PCR reactions, considering as criteria: - oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities - PCR product size - positional constraints within the source sequence - miscellaneous other constraints All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair. |
| qrna | 2.0.1 | GPL | Prototype ncRNA genefinder | QRNA uses comparative genome sequence analysis to detect conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures. |
| readseq | 19930201 | Public Domain | Reads and writes nucleic/protein sequences in various formats. | Readseq is a program for converting among several biosequence file formats, by D. Gilbert. These formats are currently understood by readseq: * ASN.1 format used by NCBI * DNAStrider, for common Mac program * EMBL, EMBL flatfile format * Fitch format, limited use * GCG, single sequence format of GCG software * GenBank/GB, genbank flatfile format * IG/Stanford, used by Intelligenetics and others * MSF multi sequence format used by GCG software * NBRF format * Olsen, format printed by Olsen VMS sequence editor. Input only. * PAUP's multiple sequence (NEXUS) format * Pearson/Fasta, a common format used by Fasta programs and others * Phylip3.2, sequential format for Phylip programs * Phylip, interleaved format for Phylip programs (v3.3, v3.4) * PIR/CODATA format used by PIR * Plain/Raw, sequence data only (no name, document, numbering) * Pretty print with various options for nice looking output. Output only. * Zuker format, limited use. Input only. |
| sim4 | 20020303 | GPL | Program to align cDNA and genomic DNA | sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other) Reference for Sim4: L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998) "A computer program for aligning a cDNA sequence with a genomic DNA sequence." Genome Research 8, 967-974. |
| wise | 2.2.0 | GPL | Comparisons of DNA and protein sequences | Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequence. Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simulta- neous prediction of say gene structure with homology based alignment. The Wise2 package was principally written by Ewan Birney, who wrote the main genewise and estwise programs. The protein comparison database search program was written by Richard Copley using the underlying Wise2 libraries. Wise2 also uses code from Sean Eddy for reading HMMs and for Extreme value distribution fitting. |
Linux reseller Bryce Coad had audiences eating out of his hand as he demonstrated the operating system running OpenOffice.org [. . .] Igor Portugal, technical head at Linux reseller Asterisk, which made its first appearance at the show in 1999, says Orix, Linfox Logistics, the Health and Disability Commission and Vita New Zealand are among its customers. Portugal collected a wad of business cards from visitors to his stand, many of which he expected to turn into sales. — ComputerWorld Expo 2002
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