Website

Website project provides to user a friendly web interface to realize searchs in annotation database, make some similarities searches, see global analyses reports, provide access to sequences annotated and some informations about the sequence analyzed

SQLite Database

When report_html_db.pl is executed, it reads the configuration files (JSON file to) and creates a SQLite database called database.db, located in Organism-Website/database.db this database file, provides some texts and storage the location of the annotation files for application, so, if you want to change this data you can use the command:

sqlite3 Organism-Website/database.db

When some page is loaded, before that, Website application access sqlite database and realize a search for texts about that page. More information about database.db gonna be provided yet.

Controllers

There is some controllers which we need to explain:

• Blast
• Root
• SearchDatabase
• Site

Root

This controller receives and process all request to main pages, it define pages that will be used and provide to them, data to be replaced from database.db. There is some functions which just exists here because aren't REST functions, it means, they are functions that provide access to download some data, access some pages that aren't processed.

/GlobalAnalyses

Loads global analyses page Don't have parameters Don't return nothing

/SearchDatabase

Loads search database page Don't have parameters Don't return nothing

/About

Loads about page Don't have parameters Don't return nothing

/Blast

Loads Blast page Don't have parameters Don't return nothing

/Downloads

Loads Download page Don't have parameters Don't return nothing

/Help

Loads help page Don't have parameters Don't return nothing

/

Loads Home page Don't have parameters Don't return nothing

/DownloadFile

This action allow the user to download a sequence file Don't return nothing

Parameters

Description

type

Tag to file to be downlaoded( 'ag' to download all genes, 'trg' to download tRNA sequences, 'rrg' to download rRNA squences, 'oncg' to download RNA sequences, 'pro' to download all nucleotidic sequences, 'ac' to download all contig sequences, 'tt' to download all transcriptional terminators sequence, 'ftb' to download feature table submission reports, 'eft' to download feature table artemis reports, 'gff' to download GFF3 reports)

/DownloadSequence

This action allow the user to download a stretch sequence
Don't return nothing

Parameters	Description
contig	Contig name
start	Start position
end	End position
reverseComplement	Do you want a reverse complement?

Site

This is a mixed REST and common controller which is composed by some functions executed by Javascript when website application is running and there is some request events to be executed and some functions that allow the user to download some files. All functions here should be executed with a GET requisition, if it's a REST request, should have in header a parameter "content-type" = "application/json".

/GetHTMLContent

Method used to get HTML content from file by filepath
Returns a Report_HTML_DB::Models::Services::BaseResponse which in response, there's the HTML content.

Parameters	Description
filepath	Filepath to HTML required inside root directory

/Components

Method used to get all Components used in annotations
Returns a Report_HTML_DB::Models::Services::BaseResponse which in response, there's a components list. Don't receive any parameter

/FileByComponentID

Method used to get file by component id
Returns compressed file with all annotations from a gene

Parameters	Description
id	Feature ID

/ViewResultByComponentID

Method used to view result by component ID
Returns annotation result

Parameters	Description
locus_tag	Feature ID
name	Component name

/ViewFileByContigAndType

Method used to view result by contig and type which type is a substring of a component name
Returns annotation result

Parameters	Description
type	Component name
contig	Contig name

/DownloadFileByContigAndType

Method used to download file by contig and type
Returns annotation result

Parameters	Description
type	Component name
contig	Contig name

/Contig

Method used to realize search by contigs, optional return a stretch or a reverse complement
Returns a Report_HTML_DB::Models::Services::BaseResponse which in response, there's an object with Contig information.

Parameters	Description
contig	Contig ID
contigStart	Start position
contigEnd	End position
revCompContig	Do you want it reverse complemented?

Blast

This REST controller execute BLAST request service

/Blast/search

This function execute a service request to execute a BLAST search and fancy_blast.pl Returns a Report_HTML_DB::Models::Services::BaseResponse which in response there is a image codified in Base64 and the HTML BLAST response.

Parameters	Description
PROGRAM	Program name (blastn, blastp, blastx, tblastn, tblastx)
DATALIB	Data lib(PMN_genome_1 for all genes - nucleotidic sequences, PMN_genes_1 for contigs in nucleotidic sequence, PMN_prot_1 for protein sequences)
QUERY_FROM	Set subsequence from
QUERY_TO	Set subsequence to
FILTER	Set filters(for low complexity use "L" value)
EXPECT	Read more here
MAT_PARAM	Read more here
UNGAPPED_ALIGNMENT	"is_set" if you want a ungapped alignment
GENETIC_CODE	Read more here
DB_GENETIC_CODE	Read more here
COST_OPEN_GAP	Read more here
COST_EXTEND_GAP	Read more here
WORD_SIZE	Word size for wordfinder algorithm (length of best perfect match)
ALIGNMENT_VIEW	Read more here
DESCRIPTIONS	Read more here
ALIGNMENTS	Read more here

SearchDatabase

This REST controller execute requests related to searchs in annotation database

/SearchDatabase/GetGene

Method used to realize search by genes
Returns a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::Feature as response

Parameters	Description
geneID	Search by genes with this locus tag
geneDescription	Search by genes with this description
noDescription	Search by genes which don't contain this description
individually	Match all terms, positive values can be "on", 1; set 0 if you don't want
featureId	Search by a list of genes with those feature ID; Should be a string with feature IDs separated by spaces
pageSize	Quantity of elements
offset	Offset of search

/SearchDatabase/GetGeneBasics

Method used to return basic data of genes from database: the beginning position from sequence, final position from the sequence, type, name
Returns a Report_HTML_DB::Models::Services::BaseResponse with a list of Report_HTML_DB::Models::Application::Feature as response.

Parameters	Description
id	Feature ID

/SearchDatabase/GetSubsequence

Method used to get subsequence stretch of gene
Returns a Report_HTML_DB::Models::Services::BaseResponse with a subsequence string as response

Parameters	Description
type	Type of sequence (CDS, or anything else)
contig	Contig's name, if you're using a type of sequence different of "CDS", contig's name is required
sequenceName	Sequence's name, if you're using a type of sequence equal "CDS", sequence's name is required
start	Start position
end	End position

/SearchDatabase/SubEvidences

Method used to get subevidences by feature ID
Returns a Report_HTML_DB::Models::Services::BaseResponse with a list of Report_HTML_DB::Models::Application::Subevidence as response

Parameters	Description
feature	Feature ID
locus_tag	Locus tag

/SearchDatabase/analysesCDS

Method used to realize search of analyses of protein-coding genes
Returns a Report_HTML_DB::Models::Services::PagedResponse with a list of feature IDs as response
The following table list key-value hash table parameters:

Parameters	Description
contig	Scalar variable with feature ID from contig
geneDesc	Scalar variable which realize search by all CDS with this description
noDesc	Scalar variable which realize search by all CDS that doesn’t have this description
individually	Scalar variable which make all terms from geneDesc and noDesc match
noGO	Scalar variable, if you don’t want to have results related to GO annotation
goID	Scalar variable with GO Identifier
goDesc	Scalar variable with GO Description
noTC	Scalar variable, if you don’t want to have results related to TCDB annotation
tcdbID	Scalar variable with TCDB ID
tcdbFam	Scalar variable with TCDB Family
tcdbSubclass	Scalar variable with TCDB subclass
tcdbClass	Scalar variable with TCDB class
tcdbDesc	Scalar variable with TCDB description
noBlast	Scalar variable, if you don’t want to have results related to BLAST annotations
blastID	Scalar variable with BLAST identifier
blastDesc	Scalar variable with BLAST description
noRps	Scalar variable, if you don’t want to have results related to RPS-BLAST annotations
rpsID	Scalar variable with RPS-BLAST Identifier
rpsDesc	Scalar variable with RPS-BLAST Description
noKEGG	Scalar variable, if you don’t want to have results related to KEGG annotations
koID	Scalar variable with KEGG Identifier
keggPath	Scalar variable with KEGG Pathway
keggDesc	Scalar variable with KEGG description
noOrth	Scalar variable, if you don’t want to see results related to orthology annotations.
orthID	Scalar variable with orthology Identifier
orthDesc	Scalar variable with orthology description
noIP	Scalar variable, if you don’t want to see results related to InterProScan annotations.
interproID	Scalar variable with InterProScan identifier
interproDesc	Scalar variable with InterProScan description
noTMHMM	Scalar variable, if you don’t want results related to TMHMM annotations.
TMHMMdom	Scalar variable with number of transmembrane domains
tmhmmQuant	Scalar variable which auxiliate search of TMHMMdom, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
noDGPI	Scalar variable, if you don’t want results related to DGPI annotations.
cleavageSiteDGPI	Scalar variable with cleavage site from DGPI
scoreDGPI	Scalar variable with score from DGPI
cleavageQuant	Scalar variable which auxiliate search of cleavageSiteDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
scoreQuant	Scalar variable which auxiliate search of scoreDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
noPreDGPI	Scalar variable, if you don’t want results related to PreDGPI annotations.
namePreDGPI	Scalar variable with name of PreDGPI
positionPreDGPI	Scalar variable with position from PreDGPI
positionQuantPreDGPI	Scalar variable which auxiliate search of positionPreDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
specificityPreDGPI	Scalar variable specifity from PreDGPI
specificityQuantPreDGPI	Scalar variable which auxiliate search of specificityPreDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
sequencePreDGPI	Scalar variable with sequence to compare with PreDGPI annotations
noBigGPI	Scalar variable, if you don’t want results related to BiGPI annotations.
pvalueBigpi	Scalar variable value from BiGPI
pvalueQuantBigpi	Scalar variable which auxiliate search of quantity BiGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
positionBigpi	Scalar variable value with the position of BiGPI annotation
positionQuantBigpi	Scalar variable which auxiliate search of position BiGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
noPhobius	Scalar variable, if you don’t want results related to Phobius annotations.
TMdom	Scalar vairable, quantity of transmembrane domains
tmQuant	Scalar variable which auxiliate search of parameter TMdom, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
sigP	Scalar variable if you want the phobius with result with signal peptide. If you don’t care: “sigPwhatever”, if you want: “sigPyes”, if you don’t want: “sigPno”
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
components	Scalar variable with annotation component names used

/SearchDatabase/trnaSearch

Method used to get a list of tRNA annotated
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::TRNASearch as response

Parameters	Description
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
tRNAaa	Scalar variable to search tRNA by amino acid
tRNAcd	Scalar variable to search tRNA by codon

/SearchDatabase/tandemRepeatsSearch

Method used to get a list of tandem repeats annotated by annotation_trf.pl
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::TRFSearch as response

Parameters	Description
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
TRFrepSeq	Scalar variable with sequence in repetition unit
TRFrepSize	Scalar variable with repetition units of bases
TRFsize	Scalar variable which auxiliate search of repetition units of bases, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
TRFrepNumMin	Scalar variable with occurrences in this min value
TRFrepNumMax	Scalar variable with occurrences in this max value

/SearchDatabase/rRNA_search

Method used to request a search for rRNA
Returns a Report_HTML_DB::Models::Services::PagedResponse with array of feature IDs of rRNA results as response

Parameters	Description
pageSize	Quantity of elements
offset	Offset of search
type	Type of rRNA
contig	Contig ID

/SearchDatabase/ncRNASearch

Execute a GET request, asking for non coding RNAs
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::NcRNASearch as response

Parameters	Description
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
ncRNAtargetID	Scalar variable with target ID from RFAM
ncRNAevalue	Scalar variable with evalue from result
ncRNAevM	Scalar variable which auxiliate search with evalue result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
ncRNAtargetName	Scalar variable with target name
ncRNAtargetClass	Scalar variable with target class
ncRNAtargetType	Scalar variable with target type
ncRNAtargetDesc	Scalar variable with target description

/SearchDatabase/transcriptionalTerminatorSearch

Execute a GET request, asking by transcriptional terminators annotations
Return a Report_HTML_DB::Models::Services::PagedResponse with Report_HTML_DB::Models::Application::TranscriptionalTerminator as response

Parameters	Description
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
TTconf	Scalar variable with transcriptional termintators with confidence score
TTconfM	Scalar variable which auxiliate search with confidence score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
TThp	Scalar variable with transcriptional terminators with hairpin score
TThpM	Scalar variable which auxiliate search with hairpin score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
TTtail	Scalar variable with transcriptional terminators with tail score
TTtailM	Scalar variable which auxiliate search with tail score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"

/SearchDatabase/rbsSearch

Execute a GET request, asking by ribosomal binding sites annotation
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::RBSSearch as response.

Parameters	Description
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
RBSpattern	Scalar variable with a sequence pattern
RBSshift	Scalar variable with "on" for true value or 0 for false, represents a search for all ribosomal binding site predictions that recommend a shift in start codon position
RBSshiftM	Scalar variable with option values, if you want upstream, value should be "neg"; if you want downstream, value should be "pos"; if you want either, value should be "both"
RBSnewcodon	Scalar variable with "on" for true value or 0 for false, represents a search for all ribosomal binding site predictions that recommend a change of start codon

/SearchDatabase/alienhunterSearch

Execute a GET request, asking by horizontal transferences annotations
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::AlienHunterSearch as response

Parameters	Description
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
AHlen	Scalar variable with length of regions predicted
AHlenM	Scalar variable which auxiliate search with length of regions predicted result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
AHscore	Scalar variable with value to get regions of score
AHscM	Scalar variable which auxiliate search with regions of score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
AHthr	Scalar variable with value to get regions of threshold
AHthrM	Scalar variable which auxiliate search with regions of treshold result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"

/SearchDatabase/geneByPosition

Execute a GET request, asking for genes by position Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::Feature as response

Parameters	Description
start	Start position
end	End position
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig

/SearchDatabase/getSimilarityEvidenceProperties

Execute a GET request, asking by similarity evidence properties from a evidence Return a Report_HTML_DB::Models::Services::BaseResponse with a hash of properties as response

Parameters	Description
feature_id	Feature ID from evidence

/SearchDatabase/getIntervalEvidenceProperties

Execute a GET request, asking by interval evidence properties from a evidence Return a Report_HTML_DB::Models::Services::BaseResponse with a list of hashs composed by key and values as a response

Parameters	Description
feature	Feature ID from evidence
typeFeature	Component name