This allows the direct use of the program without the prior download of bulky sequence files and without the need to process such files to fit a predetermined format.
This preprocessing includes: (i) download of genome sequences and gene annotations, (ii) unification of gene annotations among the set of considered strains, (iii) identification of gene families, (iv) computation of multiple alignments and identification of point mutations which constitute the input genotype data.
The following steps were performed: download of protein sequences of genes annotated on each of the following complete N. meningitidis genomes, spanning different serogroups: FAM18 (NC_008767) and 053442 (NC_010120) from serogroup C, Z2491 (NC_003116) from serogroup A, MC58 (NC_003112) from serogroup B and the capsule null strain alpha14 (NC_013016), for which the serogroup cannot be defined.
The BLAST information, including clone name, strain and tissue of origin, were stored in the MySQL EST database (MySQL version 5.027-max 5.027-max and documentation can binariesoanddocumentation A PHP (version 5.1.2) web interfacanallows user-friendly access to this information and download of all sequences in FASTA format.
The "Sequences" tab, provides options to download sequences of gene, RNA, coding sequence (CDS), protein and other sequence annotations (promoters, ESTs, regulatory elements, repeat elements etc).
FTP downloads of these sequence data have also grown from 394 downloads in 2011 to a projected 540 for 2012.
The downloading, parsing and import of gene entries, the downloading of chromosome sequences and the calculation of exon and intron sequences are described in detail in the software documentation.
The unigenes obtained as query results can be inspected individually, but also bulk downloads of the sequences, names or orthologs are allowed.
In addition to the three sections described earlier (Browse, Search and Tools) multiple approaches for downloading of TE sequences were provided by MnTEdb.
