In this section you will find how to organize data files for the application.
The SynTView software is only designed for interactive visualization of data, you have to provide the software with appropriately formatted data (genome annotations, synteny relationships, SNP data)
The next section will describe the internal formats of the files.
The Data directory must contain the Synteny files or SNP files as described just below :


Helicobacter pylori B8 example
All the genome annotation files : (ptt format file is described here)

AE000511.ptt AE017125.ptt B128.ptt CP000012.ptt CP000241.ptt CP001072.ptt CP001217.ptt CP001680.ptt CP002071.ptt CP002074.ptt CP002096.ptt CP002331.ptt CP002334.ptt FM991728.ptt FN598874.ptt -AE001439.ptt AM260522.ptt BX571656.ptt CP000153.ptt CP000538.ptt CP001173.ptt CP001582.ptt CP001816.ptt CP002073.ptt CP002076.ptt CP002184.ptt CP002332.ptt CP002336.ptt FN555004.ptt FQ670179.ptt

All the Bdbh files : (Bdbh format file is described here)

FN598874_AE000511 FN598874_CP000012 FN598874_CP001217 FN598874_CP002074 FN598874_CP002334 FN598874_AE001439 FN598874_CP000153 FN598874_CP001582 FN598874_CP002076 FN598874_CP002336 FN598874_AE017125 FN598874_CP000241 FN598874 _CP001680 FN598874_CP002096 FN598874_FM991728 FN598874_AM260522 FN598874_CP000538 FN598874_CP001816 FN598874_CP002184 FN598874_FN555004 FN598874_B128 FN598874_CP001072 FN598874_CP002071 FN598874_CP002331 FN598874_FN598874 FN5988 74_BX571656 FN598874_CP001173 FN598874_CP002073 FN598874_CP002332 FN598874_FQ670179

And a manifest filei that list all the files required (only for the web version)


Example of a genome reference compared with 39 strains to compute polymorphisms
The directory must contain the reference genome (Genome.ptt), a fasta file with the nucleic sequence of all the CDS and a manifest list file and the SNP directory

Genome.nucseq Genome.ptt liste snps

The SNP directory ('snps') contains several files containing the polymorphisms in a tabulated format (described here):

10.coverage 13.coverage 16.coverage 19.coverage 21.coverage 24.coverage 27.coverage 2.coverage 32.coverage 35.coverage 38.coverage 4.coverage 7.coverage 11.coverage 14.coverage 17.coverage 1.coverage 22.coverage 25. coverage 28.coverage 30.coverage 33.coverage 36.coverage 39.coverage 5.coverage 8.coverage 12.coverage 15.coverage 18.coverage 20.coverage 23.coverage 26.coverage 29.coverage 31.coverage 34.coverage 37.coverage 3.coverag e 6.coverage 9.coverage

and read's coverage

10.snp 12.snp 14.snp 16.snp 18.snp 1.snp 21.snp 23.snp 25.snp 27.snp 29.snp 30.snp 32.snp 34.snp 36.snp 38.snp 3.snp 5.snp 7.snp 9.snp 11.snp 13.snp 15.snp 17.snp 19.snp 20.snp 22.snp 24.snp 26.snp 28.snp 2.snp 31.snp 33.snp 35.snp 37.snp 39.snp 4.snp 6.snp 8.snp
And the list file

Optionnal files : tree.nw (phylogenetic tree in Newick format), Straingroup