The actual parsing for this is done using the People gem written by Matthew Ericson, deputy graphics editor at The Times.
After receiving the main page, the web browser will parse for the embedded objects.
Using Perl scripts, this file was parsed for the predicted protein-coding sequences and their corresponding genomic positions.
To this end gene descriptions, retrieved from BioMart, were parsed for the occurrences of these terms.
The satisfying assignments are then parsed for the output and drug vectors, and reported in the results.
The alignment files were parsed for the reads where one mate is aligned to human chromosome and another to HPV.
After that, the file containing the FPC results of the physical map was parsed for the position of BAC clones in contigs.
The chromosome number, start and end positions, and orientation were parsed for the top human BLASTN hit to the cattle assembly sequences (Additional file 5).
The contigs were parsed for the longest contributing sequence that contained patterned sequence at a particular position in the contig, where position was a window of nine nucleotides centered at the midpoint of a patterned sequence.
These were cleaved using in house PERL scripts and parsed for the identification of the microsatellite markers using the MIcroSAtellite identification (MISA) tool (http://pgrc.ipk-gatersleben.de/misa/) with default parameter setting.
