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Custom databases

Custom database configuration

It is also possible that users use custom databases or a list of NCBI protein IDs for additional genome annotation. The custom annotation is triggered with the --custom_db or --ncbi_proteins parameters. The --custom_db option accepts more than one database (in nucl/prot FASTA) at once, separated by commas. E.g. --custom_db db1.fasta,db2.fasta. The --ncbi_proteins option expects a single file containing a list of NCBI protein IDs.

Although simple, the files must follow some formatting rules in order to make it possible to summarize alignments and render reports in HTML format, that shall be available under the report_files directory.

Files in FASTA (--custom_db)

Sequence headers must follow a 5-field rule separated by "~" and spaces. The first 4 fields must be separated by "~" and the last one by one space, as exemplified below:

# Sequence header
>Database_name~~~gene/product_name/alias~~~acc.number_reference_or_identification~~~gene_product  Description

# An example with a VFDB sequence
>VFDB~~~(plc)~~~VFG037176(gb|YP_001844723)~~~[Phospholipase_C_(VF0470)]  VFG037176(gb|YP_001844723) (plc) phospholipase C [Phospholipase C (VF0470)]

Warning

Except for the Description field, the first four (DB name, gene name, gene reference and gene product) must have no whitespaces.

Note

It is very important to follow this header format in order to make it possible and easier to render summaries and reports of the BLASTn result, such as below:

List of NCBI protein IDs (--ncbi_proteins)

If users do not want to download and format input sequences, it is possible to give the pipeline a list of IDs from NCBI protein database. When given, the pipeline download the sequences and formats them in the expected way for the annotation modules. See the example below of the expected formating of this file. It is pretty simple.

WP_118891437.1
VTX70803.1
VTX49335.1
WP_005693332.1
WP_138172127.1

Expected output

When the header is followed, the summaries and reports are very well rendered such as in this example:

SEQUENCE    START   END STRAND  GENE    COVERAGE    GAPS    %COVERAGE   %IDENTITY   DATABASE    VFDB_ID PRODUCT DESCRIPTION
BNHFPCLP_00473  1   528 +   (rcsB)  1-527/651   2/3 80.8    99.43   VFDB    VFG049018(gb|YP_002920501.1)    [RcsAB_(VF0571)]     VFG049018(gb|YP_002920501.1) (rcsB) transcriptional regulator RcsB [RcsAB (VF0571)]
BNHFPCLP_00654  1   629 +   (cpsACP)    1-629/630   0/0 99.84   95.55   VFDB    VFG048985(gb|YP_002920368.1)    [Capsule_(VF0560)]   VFG048985(gb|YP_002920368.1) (cpsACP) phosphatase PAP2 family protein [Capsule (VF0560)]
BNHFPCLP_00676  1   1167    +   (ugd)   1-1167/1167 0/0 100.0   96.92   VFDB    VFG048797(gb|YP_002920350.1)    [Capsule_(VF0560)]   VFG048797(gb|YP_002920350.1) (ugd) UDP-glucose 6-dehydrogenase [Capsule (VF0560)]
BNHFPCLP_00680  1   741 +   (wzt)   1-741/741   0/0 100.0   99.46   VFDB    VFG049084(gb|YP_002920347.1)    [LPS_(VF0561)]   VFG049084(gb|YP_002920347.1) (wzt) lipopolysaccharide O-antigen ABC transport system ATP-binding component [LPS (VF0561)]
BNHFPCLP_00685  1   894 +   (wbbN)  1-894/894   0/0 100.0   98.77   VFDB    VFG049051(gb|YP_002920344.1)    [LPS_(VF0561)]   VFG049051(gb|YP_002920344.1) (wbbN) glycosyltransferase [LPS (VF0561)]
BNHFPCLP_00686  1   1131    +   (wbbO)  1-1131/1131 0/0 100.0   99.47   VFDB    VFG049040(gb|YP_002920343.1)    [LPS_(VF0561)]   VFG049040(gb|YP_002920343.1) (wbbO) glycosyltransferase family 1 protein [LPS (VF0561)]
BNHFPCLP_00770  1   624 +   (rcsA)  1-624/624   0/0 100.0   100.0   VFDB    VFG049007(gb|YP_002920216.1)    [RcsAB_(VF0571)]     VFG049007(gb|YP_002920216.1) (rcsA) transcriptional activator for ctr capsule biosynthesis [RcsAB (VF0571)]
BNHFPCLP_01728  1   936 +   (iroE)  1-936/936   0/0 100.0   99.04   VFDB    VFG044322(gb|YP_002919453)  [Sal_(VF0563)]   VFG044322(gb|YP_002919453) (iroE) siderophore esterase IroE [Sal (VF0563)]
BNHFPCLP_02092  1   543 +   (sciN/tssJ) 1-543/543   0/0 100.0   99.45   VFDB    VFG048784(gb|YP_005226619.1)    [T6SS_(VF0569)]  VFG048784(gb|YP_005226619.1) (sciN/tssJ) type VI secretion system lipoprotein TssJ [T6SS (VF0569)]

Last update: 2022-03-28