Website management


1. Constructing/Removing a website (by using a command line interface)
(1) Preparing configuration files
(1-1) With assemblies
(1-1-1) Preparing a configuraion file

# Website name (Required)

>Website_name
Example

# Input assemblies (Required)

### Path list for files in FASTA format
> Assemblies
Human ../data/example_inputs/human.fa
Mouse ../data/example_inputs/mouse.fa
Cow ../data/example_inputs/cow.fa

# Divergence times (Required)

### Example) Human-chimpanzee: near, Human-mouse: medium, Human-chicken: far
> Divtimes
Human,Mouse medium
Human,Cow medium
Mouse,Cow medium

# Resolutions (Required)

### The minimum size of synteny blocks in base pair
> Resolutions 150000,300000,400000,500000

# Gene annotations of reference (Optional)

### Path list of files in Gene transfer format(GTF)
>Annotation
Human ../data/example_inputs/Homo_sapiens.GRCh38.87.gtf.gz
Mouse ../data/example_inputs/Mus_musculus.GRCm38.87.gtf.gz

#Cytogenetic bands (Optional)

> Cytoband
Human ../data/example_inputs/Human.cytoband
Mouse ../data/example_inputs/mouse.cytoband
Cow ../data/example_inputs/mouse.cytoband

# Pre-built circos plots (Optional)

### If user wants to visualize all chromosomes/scaffolds, user should write 'all' instead of specific chromosomes.
> Circos1
resolution:150000
Human:chr1,chr3,chr5,chr6,chr8,chr12,chr15,chr19
Mouse:chr1,chr3,chr7,chr17,chr18
Cow:chr3,chr9,chr10,chr14,chr17,chr22


# Email address (Optional)

### It is used to make a contact link in published website.
> Email
User@email.com
(1-1-2) Required input data & formats

# FASTA format

>1
TTATTCCGCATCTTCTGAAGAAGATGTTCCGAATATATCCTTAGAAAGGA
GGTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCC

# GTF format

1 havana gene 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2";
1 havana transcript 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1";

# Cytoband format

chr1 0 2300000 p36.33 gneg
chr1 2300000 5400000 p36.32 gpos25
chr1 5400000 7200000 p36.31 gneg

(1-2) With synteny blocks
(1-2-1) Preparing a configuraion file

# Website name (Required)

> Website_name
Example

# Input synteny blocks (Required)

### Path list of files in synteny format
> Synteny_blocks
Human,Mouse ../data/example_inputs/human.mouse.synteny
Human,Cow ../data/example_inputs/human.cow.synteny

# Genome size files (Required)

### Path list of files in genome size format
> Genome_size
Human ../data/example_inputs/human.sizes
Mouse ../data/example_inputs/mouse.sizes
Cow ../data/example_inputs/cow.sizes

# Gene annotations of reference (Optional)

### Path list of files in Gene transfer format(GTF)
> Annotation
Human ../data/example_inputs/Homo_sapiens.GRCh38.87.gtf.gz
Mouse ../data/example_inputs/Mus_musculus.GRCm38.87.gtf.gz

# Cytogenetic bands (Optional)

> Cytoband
Human ../data/example_inputs/Human.cytoband
Mouse ../data/example_inputs/mouse.cytoband
Cow ../data/example_inputs/mouse.cytoband

# Pre-built circos plots (Optional)

### If user wants to visualize all chromosomes/scaffolds, user should write 'all' instead of specific chromosomes.
> Circos1
resolution:150000
Human:chr1,chr3,chr5,chr6,chr8,chr12,chr15,chr19
Mouse:chr1,chr3,chr7,chr17,chr18
Cow:chr3,chr9,chr10,chr14,chr17,chr22

# Email address (Optional)

###It is used to make a contact link in published website.
> Email
User@email.com
(1-2-2) Required input data & formats

# Synteny format

One line starting with a '>' sign, followd by the synteny number
The other two lines containing the coordinates and the orientation in each scaffold of pairwise alignment
(First line is only for reference chromosome(scaffold)

>1
Human.chr1:933237-58547094 +
Mouse.chr4:103313481-156255944 -

>2
Human.chr1:58654678-67136459 +
Mouse.chr4:94941999-103299247 +

# Genome size format

First column containing chromosome(scaffold) name and second column containing chromosome(scaffold) size

How to make?
[mySyntenyPortal_root]/src/third_party/kent/faSize -detailed [FASTA] > [size file]

chr1 249250621
chr2 243199373

GTF format

1 havana gene 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2";
1 havana transcript 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1";

Cytoband format

chr1 0 2300000 p36.33 gneg
chr1 2300000 5400000 p36.32 gpos25
chr1 5400000 7200000 p36.31 gneg

(2) Command lines
(2-1) Building website
User can use the 'mySyntenyPortal' perl script to build website.

Command:
./mySyntenyPortal build <parameters>

Parameter:
-conf|c=> Configuration file
-core|p=> Number of threads (default: 10)

Example:
./mySyntenyPortal build -p 10 -conf ./configurations/sample.conf
(2-2) Removing website
User can use the 'mySyntenyPortal' perl script to remove website.

Command:
./mySyntenyPortal remove <parameters>

Parameter:
-website_name|w=> Website name
-conf|c=> Configuration file

Example:
./mySyntenyPortal remove -website_name Sample_website

2. Publishing/Unpublishing a website (by using a web interface)
(1) Drawing default plots

This step is to draw plots which are used as default plots in the pubilshed website.

< SynCircos >


< SynBrowser >

(2) Publishing a website
(3) An example of a pubilshed website
(4) Published website information
<Before publishing>
<After publishing>
(5) Unpublishing a selected website

SynCircos

SynCircos draws the interactive Circos plot by using selected species and chormosomes.

1. Drawing a plot
(1) Selecting a reference species and chromosomes (or scaffolds)
(2) Selecing a target species and chromosomes (or scaffolds)
(2-1) Adding a target species
(2-2) Removing a target species
(3) Selecting a resolution of synteny blocks (Only assemblies input)
(4) Clicking 'Submit' button to draw the Circos plot
(5) An example of the Circos plot

2. Downloading a plot
(1) Selecting an image format.
(2) Clicking on 'Download' button.

SynBrowser

SynBrowser shows synthenic relationships between two chosen species with annotated genes of a reference species.
User can easily navigate the reference chromosomes by using coordinates or genes.

1. Drawing a plot
(1) Selecting a reference species and a chromosome.
(2) Selecting a target species.
(3) Selecting a resolution of synteny blocks. (Only assemblies input)
(4) Clicking 'Submit' button to draw a plot showing pairwise synthenic information.

2. Downloading a plot
(1) Selecting an image format.
(2) Clicking on 'Download' button.

3. Browsing the details of synteny blocks
(1) Obtaining information about synteny blocks
(2) Browsing gene annotation
(3) Obtaining gene information

4. Searching for a specific position in synteny blocks
(1) Selecting a reference chromosome
(2) Searching by using a query gene
(3) Searching by using a coordinate of synteny blocks