GenBank Flat File Reader

Read GenBank-formatted flat file into structure

Although the MATLAB Bioinformatics Toolbox has an endogenous GenBank file reader, genbankread(), it sometimes has difficulty reading these flat files with unexpected, but not unorthodox, formatting. This program, gbread(), is designed to replace genbankread() with a more versatile alternative. Unlike genbankread(), which expects fields to maintain strict formatting and order, gbread() blocks off each record as a cell array of text lines, searches for fields, and handles them with a switch/case design. Rather than induce a fatal error, unrecognized fields are appended to the output structure as a block of text. Benchmarks show a surprising ten-fold speed-up of gbread() over genbankread(). Unlike genbankread(), gbread() defaults to automatically parsing features, but does not sacrifice time to reading CDS entries when this option is turned off. Overall, gbread() provides enhanced versatility, reliability, speed, and convenience for reading GenBank flat files in MATLAB.