Search Results for "sql command line" - Page 24
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Showing 635 open source projects for "sql command line"
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The program siRNArules 1.0 can predict active short interfering RNA (siRNA) with a rather high efficiency (see published paper on this in RNA journal). This project aims to develop new versions, siRNArules 2.0 etc.
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hmm2gviz is a tool used for converting hidden Markov models generated by HMMER into a graph visualization using Graphviz.
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The program consgen takes multiple protein structures in PDB format and aligns them using a modified Procrustes method that aims to maximize residue similarity. The principal result is a consensus structure showing residue conservation.
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Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)
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UMD Overlapper takes a set of reads and quality data and determines which read pairs plausibly overlap; that is, it determines the pairs of reads containing subsequences that are similar enough that they may have come from overlapping parts of the genome.
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Utility to convert the binary file format from an ABI PRISM TM 377 DNA Sequencer to an xml file. New project page: https://github.com/eriksjolund/abi2xml abi2xml was migrated to Github 6 February 2020.
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birdweights is a a package of scripts to analyze data from an automated system for the measurement of mass and identification of birds at perches.
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Bio-WormBase provides a suite of software for the installation and monitoring of a WormBase mirror site.
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SeqFreed is a bioinformatics desktop. It provides efficient access to sequence data and gene features, a customizable command line interface to locally installed bioinformatic tools and flexible display of either text or images in different page modes.
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ea-fold is a platform to perform protein folding simulations by means of evolutionary algorithms. The program implements a parallelized distributed evolutionary algorithms and a flexible force field.
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...Native code (fast) and modular design: update rule, topology, time, measurement, initialization are independant. No GUI (for now...): configuration file (commented default automatically generated) overridable by command line.
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Acre calculates growing-space or stand-density of trees and creats pictures of it. It can also be used to calculate weighted Voronoi-Diagrams (splits up an area to the neares point or to the point with the greatest influence at a certain place).
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This is a collection of softwares that I have been using in my research on protein interaction network. By release them under the GPL 2.0 lience, I hope that they can be useful to others, as well.
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This is the command-line C-Language implementation of the PATOSEQ motif alignment algorithm as presented in (Bioinformatics, 18(8):1091-1101, 2002).
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VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome scale.
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DNA Repeats (biological palindromes, biological repeats, mathematical palindromes, mathematical repeats)
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MyGCAT: My Genome Collection With Assigned Taxonomy provides for the management of extremely large sequence databases and allows for the creation of taxon specific BLAST databases. Primariliy a set of PERL scripts and a HTML interface to a MySQL database
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QTL Reaper analyzes data from progeny of a genetic cross in experimental plants or animals. It seeks the location of genes that affect a heritable trait, and it is specially designed for analysis of gene expression measurements.
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Here we offer for download ClawHMMer, a streaming implementation of hmmsearch, running on commodity graphics. processors and parallel rendering clusters. The original HMMer version is located at http://hmmer.wustl.edu/ (also under GPL).
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The GenDB system for the annotation of prokaryote genomes. The Perl/MySQL/Apache based system supports cmd-line mode annotation, integrating dozens of bioinformatics tools, but also provides a user-friendly web interface for community annotation efforts
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MethylMapper is a collection of perl scripts that allow for easy viewing of methylatable sites in stretches of DNA.
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MyGenBank is a set of OpenSource software for managing a local copy of GenBank (www.ncbi.nih.gov/Genbank). It is implemented using Perl, MySQL, and Linux so that you can manage a complete or partial copy of GenBank on a computer as small as a laptop.
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In order to facilitate standardization and exchange of microarray layout, this project provides an ADF (Array design File))/MAGE-ML converter.
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Plotamber is a Perl script for an easy and automated plotting of properties derived from molecular dynamics or minimization calculations done with Amber, NAMD or Charmm.
