Accession numbers are mapped to NCBI accession numbers and the sequences are fetched from a locally downloaded nr database.
These translated sequences were fetched as amino acid sequences from stop codon to the next stop codon, stored in a database as a six-frame translated genome database.
The hg18 chromosome sequences were fetched using the get-genome program of the GMAP package [ 21].
Annotation information of unique protein sequences is fetched regularly from the NCBI GenBank completed with annotations gained from BLAST analyses or the Gluten allele database (5).
The repeat region and motifs present in sequences of selected species were fetched from the 'repeats' table of the database sequentially for retrieving identical target motifs and its sequences.
Protein sequences of integrases and toxin/antitoxin systems were fetched from Swissprot (http://www.expasy.ch/sprot/), type 2 restriction/modification systems from Rebase (http://rebase.neb.com/), and T3SS effectors from [19].
The sequences of 306 proteins in the human proteome corresponding to these anti-targets were fetched from the NCBI sequence database.
The taxa of the organisms of all Pfam family members that hit the sequence
The DNA sequences in between the Blat match limits were fetched from the browser and also analyzed for their similarity to the DEF cluster repeats by Blast and sim.
A list of all "bacterial KEGG entries" was obtained from the KEGG website (a total of 2910 entries) and corresponding protein sequences along with their annotations (functions, pathways and KO-families) were fetched from the M5nr [ 27] database.
