Gembase format

In order to allow the users running MacSyFinder on a bunch of genomes in a single run, we propose to adopt the following convention to fulfill the requirements for the “gembase db_type”. It consists in providing for each protein, both the replicon name and a protein identifier separated by a “_” in the first field of fasta headers. “_” are accepted in the replicon name, but not in the protein identifier. Hence, the last “_” is the separator between the replicon name and the protein identifier. For instance:

>PlasmidA_0001 YP_003225072.1_ | putative stcE protein
MKLKYLSCMILASLAMGAFAATAADNNSAIYFNTTQPVNDLQGGLAAEVK
FAQSQILSAHPKEGESQQHLTSLRKSLLLVRLVKADDKTPVQVEARDAND
KILGTLTLSPPSSLPDTVYHLDGVPADGIDFTPQNGTKKIINTVAEVNKL
SDASGSSIKSYLANNALVEIQTANGRWIRDMYLPQGAELEGKMVRFVSYA
GYNSTVFYGDRKVTLSVGNTLLFKYVNGQWFRSGELENNRIAYAQHTWSA
ELPAHWIVPGLNLVIKQGNLSGSLNDINVGAPGELLLHTIDIGMLTTPRG
RFDFAKDKEAHREYFQTIPVSRMIVNNYAPLHLKEVMLPTGTLLTDADPG
>PlasmidA_0002 YP_003225073.1_ | type II secretion protein EtpC
MLFFLSSRRDRNLFIKDIALKMLTPNWVLCVILLIAGYQLVSVIRHFWLT
PATSASDLSHVSVSETAVTDEHTEENFVFTLFGTASPPLSEGKVQKTTSS
LSDDLLSGGDLDVRGILYSSVTEHSVAIFAHNNRQFSLGIGEKVPGYDAT
ISAIFSDHIVINYQGKNASLPLRYDNPAKRNAQDDNNLIVGPVTTQANFR
VKNIFDIMSLSPVTVNNTLSGYRLSPGKASSLFYNAGLHDNDLAVLLNGS
ELRDTRQAKQIMKQLTELKEIKITVERDGQLYDAFIAVGEN
....
>ChromosomeA_0001 _YP_003573410.1_ | adhesin-like protein
MKKLFLFAALLMTGFAFYSCEDVVDNPAQDPAQSWNYSVSVKFADFDFNG
AVDENSVPYTYKAPTTLYVLNEENTLMGTITTDAAPAIGDYGTYAGTLTG
SIGNNLIITTKIGNDLTKQDGTLKSAIENGIVQTAEVPIKIYNANSGTLT
TASAKMDNTAAIAYTSLGYIKGGDKILFVEGNQTFEWTVNEEFDPYTSTD
LYIALPMNTDPETEYTISSDSKDGYTRGGTFKLADYPTLAAGKVSNYIGG
IPFIQTGVDLTKWDAYMRTDPNNTWYMNNINNGWPATFSQEVEDGKSFIV
TQSGPTLDSLNVVVGGVTGKEVNVTLNNIRLGKDRSINIGDKHGWVEYDG
THDIYGWGAKANVTLIGENECETLYIQCPATKKGEGTLNYKNLSIDSYGS
>ChromosomeA_0020 _YP_003573411.1_ | hypothetical protein
MKRIVLITLVSILTTFQAIAQVANGFYRVQNNASSRYITLRDNAVGTVDY
SSTNVDLSNIVTWSGFDKVKSNPASIIYVEQHDSKYDLKVQGTGIYAITG
GRTYLELRPKDSGYILAVTYNGMEGRLYDSEEDVDGEGYVKRSGNSAYQY
WSFIPVDTENNYIGLQPTVQVGDNYYGTLYASYPFKAASSGIKFYYVDAI
....
>NC_001548_0015 _YP_003225080.1_ | type II secretion protein EtpJ  (translation)
MSQQRVKGFTLLEMLLALAVFAALSISAFQVLQSGIRAHELSQDKVRRLA
ELQRGGSQIERDLMQMIPRHSRGSEGLLLAAPHLLKSDDWGISFTRNSWL
NPAGMLPRPELQWVGYRLRQQKLERLSYFYVDHPSGIAPDVRVVLEGVHA
FRLRFFVNGTWQARWDSTSILPQAVEVTLVMDDFAELTRLFLVSKETAE

This input file contains 3 replicons: PlasmidA (which 2 first protein identifiers are 0001 and 0002), ChromosomeA (which 2 first protein identifiers are 0001 and 0020) and NC_001548 (which first protein identifier is 0015).

Topology files

To be able to attribute a topology per replicon/genome when using the Gembase format, we propose the user to build a “topology file” in the form of a tabular file with two columns separated by a ”:”. The 1st column is the replicon name, and the 2nd the corresponding topology. Comments can be written after a “#”.

For example:

# comment line
PlasmidA : circular
ChromosomeA : linear
ChromosomeB : circular

Note

A topology file can be specified on the command-line with the “--topology-file” parameter.