Welcome

GBParsy is a library of functions that parses the GenBank flatfile, which is a representative and popular sequence format. The library is optimized for speed and efficient use of memory so it can rapidly parse large sequence such as Arabidopsis chromosome for genomic analysis. GBParsyPy is additional version of GBParsy for the Python. GBParsyPy adopted GBParsy as a core parser so GBParsyPy inherited all of its features from GBParsy.

Current Status

Version 0.6.1 of GBParsy and GBParsyPy is stable and is recommended for all users.

Changes

• Version 0.5.4 (Feb. 29, 2008) The project name is changed from GBFP to GBParsy. However, we would not change the program name in order to prevent confusion.
• Version 0.5.5 (Apr. 30, 2008) Fixed segmentation fault for a sequence containing a too long note, such as NC_003070 (Arabidopsis thaliana chromosome 1, complete sequence) version 6.
• Version 0.5.6 (May 14, 2008) Checked GBParsy by Valgrind for 2660 chromosome, plasmid and organelle sequences downloaded from GenBank and fixed a few memory leak bugs (Valgrind logs).
• Version 0.5.7 (Jun 25, 2008)
• Added medline and remark entry in the reference data
• Increased flexibility to parse LOCUS line in safety
• Added new option(-s) to seqext and seqext.py to search qualifier data
• Version 0.6.0 (July 10, 2008) Added a Python class, gbparsy, which generates a SeqRecord instance of BioPython from a parsed result.
• Version 0.6.1 (July 26, 2008)
• Fixed memory leaks of GBParsyPy
• Increased compatibility with SeqRecord of BioPython
• Changed Python example for new GBParsy class

Publication

• T.-H. Lee, Y.-K. Kim and B.H. Nahm (2008) GBParsy: A GenBank flatfile parser library with high speed. BMC Bioinformatics, 9:321.

Contact

If you have comments, questions and suggestions to the GBParsy, please use Wiki or Issue system or send a mail to thlee@bio.mju.ac.kr.