ORFer

ORFer extracts open reading frames (ORFs) from protein sequences in NCBI GenBank XML files for retrieval and management in functional genomics workflows.

Key Features:

• Sequence retrieval: Retrieves sequences from NCBI GenBank XML using GI identifiers or accession numbers.
• Open reading frame extraction: Extracts the ORF corresponding to protein sequences from GenBank XML and translates frames to amino acid sequences.
• Annotations: Parses and retrieves sequence names, organism details, and sequence completeness metadata from GenBank XML entries.
• Database integration: Stores retrieved sequences and associated features in a local SQL database.
• Export formats: Exports sequences as FASTA or tab-delimited text files.
• Implementation: Implemented as a Java-based program.

Scientific Applications:

• Functional genomics: Enables retrieval and management of ORFs for functional genomics analyses.
• Cloning and recombinant protein expression: Provides sequence and annotation information required for cloning and recombinant expression workflows.

Methodology:

Sequence requests by GI or accession number; parsing of NCBI GenBank XML; extraction of ORFs corresponding to protein sequences; translation of coding frames; retrieval of sequence annotations; storage in a local SQL database; export to FASTA or tab-delimited text.