Phoenix is a non-validating C++ parser for EMBL-Bank flat files.
EMBL Bank Sequence Nucleotide Database
EMBL-Bank constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications.
The database is produced in an international collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ). Each of the three groups collects a portion of the total sequence data reported worldwide, and all new and updated database entries are exchanged between the groups on a daily basis.
The format of EMBL-Bank flat files is described in the EMBL User Manual, while the format of the EMBL Feature Table element is described in the Feature Table Definition document.
The Parser
Phoenix main goal is to provide the bioinformatics community with a publicly available parser for EMBL flat files. The parser has been designed for use in C++ programs running under either Windows or Linux and at present is capable to quickly and efficiently parse the largest publicly available flat files (ex: files containing full genome or chromosome sequences) even when running under ordinary PC hardware.
Phoenix recognizes all of the public EMBL-Bank line types including the line types used in TPA and CON (constructed) entries. Phoenix also performs fine grained and reliable parsing of EMBL Feature Table location strings and is able to correctly disambiguate between the various recognized publication types.
Supported environments
Phoenix is written in standard C++. Therefore you need a fairly standard compliant C++ compiler to build its sources. At present the following compiler/platforms are supported:
| Platform | Compiler |
|---|
| Windows | Microsoft Visual C++ 2005 |
| Linux | g++ 3.3 or better |
Using Phoenix with non C++ programs
Phoenix is a C++ parser, so you cannot directly use Phoenix in Perl or Java programs. You can however use Phoenix to convert EMBL flat files into some suitable XML format and then read the resulting XML files using whatever XML parser is available in your language.
Learning Phoenix
A few example applications are bundled with the standard distribution. Please refer to the README file for further information.
As of release 1.0 a tutorial application has also been included.
Downloading Phoenix
Phoenix sources can be downloaded from bioinformatics.org using any Subversion client. Please refer to the following page for further informations about accessing Phoenix sources using Subversion, or click here to use Bioinformatics.org web interface to Subversion to browse individual source files.
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