Search Results for "open any file" - Page 3

... to the farthest sequences from the ends). Ambiguities (things like R, Y, N, W, etc. in a DNA sequence) can be treated like: - consider ambiguities as always different; - consider ambiguity as partially different (e.g. R would be 0.5 different from A or G); - ignore ambiguities in each pairwise comparison; - remove all columns, globally, that show any ambiguity. Pontos was written in Linux, but should run in any system where Java works. Pontos is licensed under the GPL version 3.

Index biological data (genbank sheets, Uniprot...) in a Solr indexer, with index shard support and provides a query interface. Project goal is to create a virtual image with indexer and web interface to query and visualize biological data.

A new open-source tool that integrates pipeline automated identification and phylogenetic studies of microbial communities using genes sequences

SeqAnt is an open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform.

This is a multi-threaded Java program that tries to maximise CPU utilization by separating and distributing the computational part of the work from the file reading and writing part by using separate threads.

Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.

PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.

mmView is the web based viewer of macromolecular Crystallographic Information File (mmCIF) format. Online ready-to-use version is available at http://ich.vscht.cz/~cechp/mmcif/ or http://ich.vscht.cz/projects/mmview/

A simple tool to import the diff, gtf and tracking files from cufflinks, cuffcompare, cuffdiff into a new sqlite database for data mining.

Adjusting PKL-Files derived from MS-experiments. The development of the project has been MOVED TO https://github.com/binfalse/adjustpkl

This is bionically project.

FunctSNP is an R interface to an SQL database for linking single nucleotide polymorphisms (SNPs) to functional knowledge. FunctSNP should work on any OS on which R runs.

Metmask has moved to github http://github.com/hredestig/metmask Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.

--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE-- The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.

BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.

Anna is lightweight Java framework to build pipeline systems of any kind. It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.

Ruby Research Wiki (RRiki) can be used to keep notes and organize references for research. It uses a browser interface, an intuitive plain text formatting language (markdown), and facilities to cross-reference and hierarchically organize notes

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

D-finder is a bioinformatic search algorithm for the identification of D-sites in JNK interacting proteins. The algorithm is a combination of pattern matching and a hidden markov model (HMM) based on a training set of known JNK D-sites.

T-RFPred, Terminal-Restriction Fragment Prediction Tool, is a group of Perl scripts that will help researchers to identify the profile peaks of a T-RFLP fingerprint using clone libraries of partially sequenced 16S rRNA genes from the same sample.

Inter University Multi-Modal Imaging

The goal of Picklist Editor is to display and modify pick lists before spot picking (in proteomics).

A repository linking to eight Bioinformatics Resource Centers (BRCs) sponsored by the NIAID. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of bioterrorism

JRasterCreator allows you to easily & visually build a raster file for the mass spectrometry instrument Bruker Daltonics MS ultraflex II by clicking on various spots/locations.

The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader.