ORFer - retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files

Background: Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. Results: A Java program was developed for retrieval of protein and nucleic acid sequences and annotations from NCBI GenBank, using the XML sequence format. Annotations retrieved by ORFer include sequence name, organism and also the completeness of the sequence. The program has a graphical user interface, although it can be used in a non-interactive mode. For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation. ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers. It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosome...

• Type: Journal
• Year: 2002
• Where: BMCBI
• Authors: Konrad Büssow, Steve Hoffmann, Volker Sievert
• Keywords: BMCBI 2002, Large Sets, Open Reading Frames, Proteins