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Viral Databases for VIGOR4

This repository contains viral reference databases and configurations for use with VIGOR4

Organization

The viral database contains three kinds of files: the viral databases themselves, virus specific configuration files and mature peptide databases.

Viral Database Files

The viral databases are simple fasta files.

Configuration Files

Each viral database may optionally have its own VIGOR4 .INI configuration file which overrides the default settings for that virus and matched genes. By default, VIGOR4 looks for a virus specific configuration file by appending the .ini suffix. For example, the Flu A database is named "flua_db" and the flua configuration files is "flua_db.ini"".

Configuration Sections

Any configuration parameters set outside of a section are defaults for the virus. The configuration file may also contain one or more gene specific sections. These gene specific sections should be named gene:GENE_NAME.

Configuration Parameters

Below is a list of the configuration parameters that may be set in the deflines of the viral databases or in the virus specific configuration files. The list was produced by using the --list-config-parameters option to VIGOR4 which is the recommended way to get the most update list of settable parameters.

alignment_score_factor

Environment variable:          VIGOR_ALIGNMENT_SCORE_FACTOR
System.property:               vigor.alignment_score_factor
Settable levels                virus config,gene config/variant
Description:                   Weight of alignment score in evaluating alignment

alternate_startcodon

Environment variable:          VIGOR_ALTERNATE_STARTCODON
System.property:               vigor.alternate_startcodon
Settable levels                gene config/variant
Description:                   Alternate start codons for gene. Format is CODON[,CODON,..]

circular_genome

Environment variable:          VIGOR_CIRCULAR_GENOME
System.property:               vigor.circular_genome
Settable levels                virus config,gene config/variant
Note:                          This parameters is currently unimplemented
Description:                   When this parameter is set to TRUE, VIGOR consider the genome as circular, enabling annotating genes spanning both ends of the sequence (which would be continuous when circularized).

complete_genome

Environment variable:          VIGOR_COMPLETE_GENOME
System.property:               vigor.complete_genome
Settable levels                virus config,gene config/variant
Note:                          This parameters is currently unimplemented
Description:                   When this parameter is set to TRUE, VIGOR assumes that the sequence represents the whole genome and all the genes must be present (unless a gene has the is_optional attribute)

excludes_gene

Environment variable:          VIGOR_EXCLUDES_GENE
System.property:               vigor.excludes_gene
Settable levels                gene config/variant
Description:                   Gene/sequence-level attribute describing the incompatibility of presence of two or more alternate genes (generally used only in large DNA viruses).

frameshift_sensitivity

Environment variable:          VIGOR_FRAMESHIFT_SENSITIVITY
System.property:               vigor.frameshift_sensitivity
Settable levels                virus config,gene config/variant
Note:                          This parameters is currently unimplemented
Description:                   Dictates the sensitivity VIGOR should use in handling frame-shifts. Accepted values: 0, 1, 2, with 2 being the strictest, forcing VIGOR to create pseudogenes and raising error messages whenever a perfect model for a given gene cannot be created (this is used most for validating assemblies).

is_optional

Environment variable:          VIGOR_IS_OPTIONAL
System.property:               vigor.is_optional
Settable levels                gene config/variant
Description:                   This parameter works in combination with complete_genome and frameshift_sensitivity: if it is set to TRUE, the absence of that particular gene for which is set suppresses the stricter behavior set by the use of the other parameters.

is_required

Environment variable:          VIGOR_IS_REQUIRED
System.property:               vigor.is_required
Settable levels                gene config/variant
Description:                   By setting this parameter to TRUE, VIGOR will produce an error message in the case it cannot create a valid gene model for that given gene.

leakystop_notFound_score

Environment variable:          VIGOR_LEAKYSTOP_NOTFOUND_SCORE
System.property:               vigor.leakystop_notFound_score
Settable levels                virus config,gene config/variant
Description:                   Weight to be assigned to the gene model candidates scoring when an expected leaky stop codon is not found (note: in some viruses the leaky stop codon is not always present).

leakystop_score_factor

Environment variable:          VIGOR_LEAKYSTOP_SCORE_FACTOR
System.property:               vigor.leakystop_score_factor
Settable levels                virus config,gene config/variant
Description:                   Weight for scoring leaky stops for gene model selection.

matpepdb

Environment variable:          VIGOR_MATPEPDB
System.property:               vigor.matpepdb
Settable levels                gene config/variant
Description:                   Location and name of the mature peptides reference database (e.g. matpepdb=<vigordata>/flua_ha_mp)

mature_pep_mincoverage

Environment variable:          VIGOR_MATURE_PEP_MINCOVERAGE
System.property:               vigor.mature_pep_mincoverage
Settable levels                virus config,gene config/variant
Description:                   Minimum percent coverage of the sequence of the reference mature peptide to consider the prediction valid.

mature_pep_minidentity

Environment variable:          VIGOR_MATURE_PEP_MINIDENTITY
System.property:               vigor.mature_pep_minidentity
Settable levels                virus config,gene config/variant
Description:                   Minimum percent identity between the sequence of the reference mature peptide and the sequence of the candidate mature peptide.

mature_pep_minsimilarity

Environment variable:          VIGOR_MATURE_PEP_MINSIMILARITY
System.property:               vigor.mature_pep_minsimilarity
Settable levels                virus config,gene config/variant
Description:                   Minimum percent similarity between the sequence of the reference mature peptide and the sequence of the candidate mature peptide. Note: similarity is calculated using compatibility values found in Blosum40 distance matrix

max_aa_overlap

Environment variable:          VIGOR_MAX_AA_OVERLAP
System.property:               vigor.max_aa_overlap
Settable levels                virus config,gene config/variant
Description:                   Maximum number of proteins that may overlap for alignment fragments to be considered compatible when generating a gene model

max_align_merge_aa_gap

Environment variable:          VIGOR_MAX_ALIGN_MERGE_AA_GAP
System.property:               vigor.max_align_merge_aa_gap
Settable levels                virus config,gene config/variant
Description:                   Maximum number of proteins in a gap between two alignments to consider them for merging.

max_gene_overlap

Environment variable:          VIGOR_MAX_GENE_OVERLAP
System.property:               vigor.max_gene_overlap
Settable levels                virus config,gene config/variant
Description:                    In reporting gene models, maximum overlap of genes allowed.

max_intron_size

Environment variable:          VIGOR_MAX_INTRON_SIZE
System.property:               vigor.max_intron_size
Settable levels                virus config,gene config/variant
Description:                   Maximum sequence length of an intron

max_nt_overlap

Environment variable:          VIGOR_MAX_NT_OVERLAP
System.property:               vigor.max_nt_overlap
Settable levels                virus config,gene config/variant
Description:                   Maximum number of nucleotides that may overlap for alignment fragments to be considered compatible when generating a gene model

min_functional_len

Environment variable:          VIGOR_MIN_FUNCTIONAL_LEN
System.property:               vigor.min_functional_len
Settable levels                gene config/variant
Description:                   Minimum functional length for a protein (expressed in aa) to be functional: if a premature stop codon makes it shorter than that, it should be annotated as pseudogene.

min_gene_coverage

Environment variable:          VIGOR_MIN_GENE_COVERAGE
System.property:               vigor.min_gene_coverage
Settable levels                virus config,gene config/variant
Description:                   Minimum coverage of genes

min_intron_size

Environment variable:          VIGOR_MIN_INTRON_SIZE
System.property:               vigor.min_intron_size
Settable levels                virus config,gene config/variant
Description:                   Minimum sequence length of an intron

min_missing_AA_size

Environment variable:          VIGOR_MIN_MISSING_AA_SIZE
System.property:               vigor.min_missing_AA_size
Settable levels                virus config,gene config/variant
Description:                   Minimum number of proteins missing in a given alignment to search for missing exons.

min_pseudogene_coverage

Environment variable:          VIGOR_MIN_PSEUDOGENE_COVERAGE
System.property:               vigor.min_pseudogene_coverage
Settable levels                virus config,gene config/variant
Note:                          This parameters is currently unimplemented
Description:                   Minimum percentage of coverage in the alignment between candidate pseudogene and reference protein, based on the longest of the two.

min_pseudogene_identity

Environment variable:          VIGOR_MIN_PSEUDOGENE_IDENTITY
System.property:               vigor.min_pseudogene_identity
Settable levels                virus config,gene config/variant
Note:                          This parameters is currently unimplemented
Description:                   Minimum percentage of identity in the alignment between candidate pseudogene and reference protein, based on the longest of the two.

min_pseudogene_similarity

Environment variable:          VIGOR_MIN_PSEUDOGENE_SIMILARITY
System.property:               vigor.min_pseudogene_similarity
Settable levels                virus config,gene config/variant
Note:                          This parameters is currently unimplemented
Description:                   Minimum percentage of similarity in the alignment between candidate pseudogene and reference protein, based on the longest of the two.

min_seq_gap_length

Environment variable:          VIGOR_MIN_SEQ_GAP_LENGTH
System.property:               vigor.min_seq_gap_length
Settable levels                virus config,gene config/variant
Description:                   Minimum number of undefined nucleotides (i.e. Ns) to consider it a sequencing gap.

noncanonical_splicing

Environment variable:          VIGOR_NONCANONICAL_SPLICING
System.property:               vigor.noncanonical_splicing
Settable levels                virus config,gene config/variant
Description:                   List of alternative splicing donor and acceptor sequence pairs. Format: noncanonical_splicing=donor+acceptor,donor+acceptor,... (e.g. noncanonical_splicing=AA+GT)

note

Environment variable:          VIGOR_NOTE
System.property:               vigor.note
Settable levels                virus config,gene config/variant
Description:                   Information associated to a gene or protein variant (to be reported in the .tbl and GFF 3 outputs).

ribosomal_slippage

Environment variable:          VIGOR_RIBOSOMAL_SLIPPAGE
System.property:               vigor.ribosomal_slippage
Settable levels                gene config/variant
Description:                   Ribosomal slippage. Format is ribosomal_slippage=offset/frameshift/regex (e.g. ribosomal_slippage=-7/+1/[BDHKNTWY][BCHMNSVY][BCHMNSVY][BDHKNTWY][BDHKNTWY][BDHKNTWY][BCHMNSVY][BDGKNRSV][BCDHKMNSTVWY][BCHMNSVY])

rna_editing

Environment variable:          VIGOR_RNA_EDITING
System.property:               vigor.rna_editing
Settable levels                gene config/variant
Description:                   RNA editing. Format is rna_editing=offset/regex/insertion string/note (e.g. rna_editing=0/GGGG/[ARWMDHVN][ARWMDHVN][ARWMDHVN][ARWMDHVN][GRSKBDVN][GRSKBDVN][GRSKBDVN]/four non-templated G's inserted during transcription)

shared_cds

Environment variable:          VIGOR_SHARED_CDS
System.property:               vigor.shared_cds
Settable levels                gene config/variant
Description:                   List of other genes (gene symbols) sharing the same region of the viral genome. Format: shared_cds=Gene1_ID,Gene_2ID (e.g. shared_cds=NSP1-2; shared_cds=NSP1-1,NSP1-3)

splice_form

Environment variable:          VIGOR_SPLICE_FORM
System.property:               vigor.splice_form
Settable levels                virus config,gene config/variant
Description:                   Describes the expected gene structure with actual lengths of exons and introns of the reference protein aligned back to its originating genome (or the closest possible genome, if the original one is not available). Format: e\d+(i-?\d+e\d+)* The string always starts and ends with exons. (e.g. splice_form="e26i686e268"; splice_form="e1656") Note: given that this parameter is specific for each single isoform, it is allowed only on the sequence header.

splicing_score_factor

Environment variable:          VIGOR_SPLICING_SCORE_FACTOR
System.property:               vigor.splicing_score_factor
Settable levels                virus config,gene config/variant
Description:                   Weight to apply on splice sites (e.g. canonical v.s. non-canonical, how far from expected location, etc.) in the scoring of gene models.

start_codon_search_window

Environment variable:          VIGOR_START_CODON_SEARCH_WINDOW
System.property:               vigor.start_codon_search_window
Settable levels                virus config,gene config/variant
Description:                   Number of nucleotides before and after a candidate site to check for a start codon

start_codons

Environment variable:          VIGOR_START_CODONS
System.property:               vigor.start_codons
Settable levels                virus config,gene config/variant
Description:                   Comma separated list of expected start codons

start_score_factor

Environment variable:          VIGOR_START_SCORE_FACTOR
System.property:               vigor.start_score_factor
Settable levels                virus config,gene config/variant
Description:                   Weight to apply on start codons (e.g. canonical v.s. non-canonical, how far from expected location, etc.) in the scoring of gene models.

stop_codon_readthrough

Environment variable:          VIGOR_STOP_CODON_READTHROUGH
System.property:               vigor.stop_codon_readthrough
Settable levels                gene config/variant
Description:                   Format is amino acid/offset/regex (e.g.stop_codon_readthrough=-11/R/[NATC][NATC][NT][NG][NA][NC][NTG][NAG][NATG][NATCG][NTC][NAG][NAG])

stop_codon_search_window

Environment variable:          VIGOR_STOP_CODON_SEARCH_WINDOW
System.property:               vigor.stop_codon_search_window
Settable levels                virus config,gene config/variant
Description:                   Number of nucleotides before and after a candidate site to check for a stop codon

stop_score_factor

Environment variable:          VIGOR_STOP_SCORE_FACTOR
System.property:               vigor.stop_score_factor
Settable levels                virus config,gene config/variant
Description:                   Weight to apply on stop codons (e.g. how far from expected location, etc.) in the scoring of gene models.

tiny_exon3

Environment variable:          VIGOR_TINY_EXON3
System.property:               vigor.tiny_exon3
Settable levels                gene config/variant
Description:                   Tiny exon 3. Format is regex:[offset]

tiny_exon5

Environment variable:          VIGOR_TINY_EXON5
System.property:               vigor.tiny_exon5
Settable levels                gene config/variant
Description:                   Tiny exon 5. Format is regex:[offset]

Mature Peptide Files

Current status

Mammarenavirus The databases are in the process of migration from VIGOR3 to VIGOR4, but the following virus are considered production ready: