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.
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)]