3D Genome Tuner User Manual-2.1.0scape3d.sourceforge.net/3DGenomeTunerUserManual.pdf · 2011. 4. 26. · Open Files: Import one or more sequences into 3D Genome Tuner 3. Rotate Left:

3D Genome Tuner User Manual Version: 2.1.0 2009-02-09

Contents

Introduction......................................................................................................................................2

Highlights .........................................................................................................................................2

System Requirements ...................................................................................................................2

Installation .......................................................................................................................................3

Menus and Toolbar.........................................................................................................................3

Toolbar ......................................................................................................................................3

Open File...................................................................................................................................4

Open Files .................................................................................................................................4

Browse Bacteria Genomes ........................................................................................................4

Export Image.............................................................................................................................4

Append > Genome ....................................................................................................................4

Append > CDS..........................................................................................................................4

Append > Region ......................................................................................................................5

Append > CDS Classification ...................................................................................................6

Append > Genome Comparison > BLAST...............................................................................7

Append > Genome Comparison > MUMmer ...........................................................................7

Append > Genome Comparison > Mauve ................................................................................8

Pie Selection..............................................................................................................................8

Reveal Hotspots ........................................................................................................................9

Settings and Preference.............................................................................................................9

Layout ...............................................................................................................................9

CDS.................................................................................................................................10

RNA ................................................................................................................................10

Chart................................................................................................................................11

BLAST............................................................................................................................11

Preference........................................................................................................................11

CDS Classification Profiles ....................................................................................................12

COG ................................................................................................................................12

GO...................................................................................................................................12

Color Gradient.................................................................................................................12

User Interface ...............................................................................................................................13

Navigation Window ................................................................................................................13

Local Window.........................................................................................................................13

Chart Window .........................................................................................................................14

Sequence Window...................................................................................................................14

Alignment Window.................................................................................................................14

Magnify Window ....................................................................................................................14

Linear Chart Window..............................................................................................................15

Examples .......................................................................................................................................15

Import Sequence Files.............................................................................................................15

Import CDS.............................................................................................................................16

Import COG ............................................................................................................................16

Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.

Import regions .........................................................................................................................16

Import BLAST........................................................................................................................16

Import MUMmer.....................................................................................................................17

Copyright .......................................................................................................................................17

Contact...........................................................................................................................................17

Introduction

Thank you for choosing 3D Genome Tuner, which draws circular genome map and enables

viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment,

making it a powerful tool in genome studies and demonstrations.

Highlights

3D Genome Tuner is a novel tool which provides comparative views on multiply circular maps.

The comparisons focus on three levels: the statistical level, gene level and genomic level. 3D

Genome Tuner use easy-to-get formats such as GenBank, EMBL, FASTA and use tab-delimited

textual files to expand existing annotations and present them on the canvas. Rather than drawing

static images, 3D Genome Tuner lets you manipulate every thing, change the aspect of any track

or use whatever color you like.

System Requirements

Recommended Specification

CPU: Pentium 4 2.0Ghz or Athlon 2000+


RAM: 512MB RAM

GRAPHICS: OpenGL 1.1 compatible 16 MB 3D accelerated video card

DISPLAY: 1024 x768 resolution or higher, 16-bit or higher color

OTHER REQUIREMENTS: Mouse or tablet

Installation

Before using 3D Genome Tuner, you need to make sure you have Java installed. You can get the

latest stable release of Java from Sun Microsystems. Also note 3D Genome Tuner require JDK

1.6.0 or higher.

Once you have installed Java, you still need to install JOGL (Java bindings for OpenGL API with

OpenGL 1.5 specification) to run 3D Genome Tuner, which can be download at

https://jogl.dev.java.net/.

Follow these instructions when installing JOGL:

1. For Windows users, you need to download JSR-231 1.1.1 binaries for Windows/x86, unzip

the package and copy jogl.jar and gluegen-rt.jar to jdk1.6.0/lib under you Java directory. and

the dlls to jre1.6.0/bin and jdk1.6.0/bin under you Java directory. or your

Windows/System32 directory.

2. For Linux users, you need to download JSR-231 1.1.1 binaries for your Linux variant or

compile it yourself. Extract the files and place jogl.jar and gluegen-rt.jar to your

CLASSPATH and put the ".so" library files in one directory, e.g. "/usr/local/lib/jogl/", where

you can access.

Also see this topic if you have problems on installing JOGL or fail to launch 3D context.

http://www.cs.gmu.edu/~jchen/graphics/jogl/notes/joglSetup.html

Menus and Toolbar

Toolbar

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

1. New Session: Begin a new session.

2. Open Files: Import one or more sequences into 3D Genome Tuner

3. Rotate Left: Rotate one or all of the genomic maps around Y axis clockwise.

4. Rotate Right: Rotate one or all of the genomic maps around Y axis counter-clockwise.

5. Rotate Up: Move the camera upward.

6. Rotate Down: Move the camera downward.

7. Refresh: Redraw the graph in the main window.

8. Zoom In: Zoom the camera in towards the maps.

9. Zoom Out: Zoom the camera away from the maps.

10. Hand Tool: Grab and drag the image to show more stuff.

11. Flat View: Turn 3D circular map into flat map, or vice versa.


12. Stretch: Increase the space between maps.

13. Shrink: Decrease the space between maps.

14. Pie Selection: Draw a pie selection on the selected map.

15. Reveal Hotspots: Draw pie selections on the all circular maps which could reflect notable

changes.

16. Options: Change the general appearance and color of circular map as well as 3D Genome

Tuner performance.

Open File

Use this command to open one sequence. The

following formats are support by 3D Genome

Tuner: EMBL, GenBank or FASTA. After

loading the EMBL or GenBank files,

annotations will be parsed by 3D Genome

Tuner. However, FASTA files have no

annotations, additional information such as

genes and customized regions should be added

through the use of Append > CDS or Append

> Region

Open Files

Use this command to open more than one

sequence at a time. The sequences are drawn

in stack in the order specified in the list box.

User press the Add button to select the path of

the sequence, uses the Up, Down to move the

sequence in the list box.

Browse Bacteria Genomes

This command opens a dialog which shows a

list of all complete bacterial genomes referred

to the NCBI ftp site. Double click a strain and

all sequenced species open up. Select one

sequence file and click the Download button,

then this file will be downloaded to the

temporary file path where you specified in the

Preference option. After the download process

is completed, you will be prompted to open

this file and add to the canvas.

Export Image

This command opens a dialog prompting for a

file name where the current drawing will be

saved. On hit OK button, a JPEG image fits

the size of current graph will be created under

that directory.

Append > Genome

Use this command to open a file contains

sequence. Once the file is imported, a circular

map will be displayed under the last genome

map.

Append > CDS

This command opens a wizard dialog leading

user to append a tab-delimited or

space-delimited textual file which contains

CDS positions and information. First select


which genome the CDS genes will be

appended to in the combo box. The columns

of list are pre-defined in the program and can

be specified in the wizard. Typically, a record

of CDS should contain at least 4 columns,

these are the name (locus tag), begin position,

end position and strand (‘+’ for plus strand, ‘-’

for minus strand) in the genome. If the list file

contains title, user can choose to skip the title

by checking Has Title checkbox. If records of

CDS contain COG information, the column

which information of COG is located can be

specified, 3D Genome Tuner will render CDS

genes in the color representing their COG

categories.

In the next step, user will be prompted to

specify the radius and width of the CDS ring,

as well as whether draw CDS genes in

polygons or in lines. The colors of CDS genes

can be obtained from files or by their order.

3D Genome Tuner reads tab-delimited or

space-delimited textual file contains color

definitions, either encoding colors in a

hexadecimal format such as #FF0000, or

providing their COG code (in one character).

Both files should be indexed by name (locus

tag) of CDS.

The final step aids user to input additional

information for the CDS genes from

tab-delimited or space-delimited textual file.

The columns of list can be specified, too. User

chooses path of the file by pressing the

Browse button. If the additional information is

included in the file inputted at the first step,

user could choose to use previous CDS list file

and specify the column order in that file. The

CDS information is shown as tool tips when

cursor moves to that CDS in navigation

window. If no additional information is

needed to display, user can choose to skip this

step by selecting No additional information.

Append > Region

This command opens a wizard dialog leading

user to append a tab-delimited or

space-delimited textual file which contains

genomic regions. First select which genome

the regions will be appended to in the combo

box. The regions are drawn in separate rings

and can be used to illustrate homologous or


unique segments in the genome. The columns

of list are pre-defined in the program and can

be specified in the wizard. Typically, a record

of region should contain at least 3 columns,

these are the begin position, end position and

strand in the genome. By checking Auto

Generate ID, 3D Genome Tuner set ID for

each region by line numbers in the file. If user

gave each region an ID, the column contains

ID can be specified.

In the next step, user will be prompted to

specify the radius and width of the region ring

as well as colors for each region. The colors of

regions can be obtained from files or by their

ID. 3D Genome Tuner reads tab-delimited or

space-delimited textual file contains color

definitions. Colors are encoded in a

hexadecimal format such as #ff0000 and

indexed by their ID.

Append > CDS Classification

l COG: Clusters of Orthologous Groups of

proteins (COG) provide a mean to

classify CDS, 3D Genome Tuner can

render CDS genes in the color

representing their COG categories.

GenBank or EMBL format sequence

doesn't have COG in their feature tables,

so COG must be supplied from additional

files. First select which genome the COG

information will be appended to in the

combo box, then choose path of the file

by pressing the Browse button. The file

should contain one or two columns, if

CDS genes are indexed by their locus tag,

the first column should be locus tags and

the second column should be COG codes

(in one character), otherwise the COG

information is appended by the order

which CDS genes were inputted.

l GO: Gene Ontology (GO) is another way

to classify CDS, 3D Genome Tuner can

render CDS genes in the color

representing their GO categories.

GenBank or EMBL format sequence

doesn't have GO in their feature tables, so

GO must be supplied from additional

files. First select which genome the GO

information will be appended to in the

combo box, then choose path of the file

by pressing the Browse button. The file

should contain one or two columns, if

CDS genes are indexed by their locus tag,

the first column should be locus tags and

the second column should be GO codes

(in one character), otherwise the GO

information is appended by the order

which CDS genes were inputted.


Append > Genome

Comparison > BLAST

BLAST: This command opens a wizard dialog

leading user to append the output from

BLAST program run with "-m 8" parameter.

The Query Genome (which is the input when

you ran BLAST program) and Reference

Genome (which is the database when you ran

BLAST program) should also be set in the

combo box. Once the file is set, user goes to

the next step to choose which line between

homologous gene is displayed, user can

choose one of the following options:

l Show all BLAST links immediately:

Once user finished importing the BLAST

output, all the lines linking homologous

gene are displayed.

l Do not show BLAST links: Once user

finished importing the BLAST output,

the homologous pairs are stored in the

navigation window, but the links are not

displayed. If links cover up other things

on the graph, user can choose this option

and show links by clicking the items

under “Orthologous Pairs” to display

links one at a time.

l Show links between different genes: By

choosing this option, only the line linking

genes with different locus tag will be

displayed. Since locus tags are different

in each genome, this option is only useful

when comparing genes from the same

genome. Locus tag from different

genome should be converted to the same

locus tag if you intend to use this option.

l Show one link in this interval: By

choosing this option and specify the

interval below, 3D Genome Tuner draw

only one link in this interval, which is

useful when user only wants to see the

trends and lines cover up other things on

the graph.

Append > Genome Comparison > MUMmer

Use this command to append an alignment result generated by NUCmer in MUMmer package.

NUCmer is used for finding maximal unique matches between multiple closely related nucleotide

sequences. The output should be parsed by show-coords command first, which converts the output

to textual file contains a summary of coordinates, percent identity, etc. of the alignment regions.

Typically, the format of result should be looking like this:

/ NC_003143.fas / NC_005810.fas

NUCMER

[S1] [E1] | [S2] [E2] | [LEN1] [LEN2] | [%IDY] | [TAGS]


==================================================================================

251 14059 | 1 13824 | 13809 13824 | 99.89 | NC_003143 NC_005810

251 93346 | 1 93142 | 93096 93142 | 99.94 | NC_003143 NC_005810

12291 17409 | 3506286 3501168 | 5119 5119 | 99.84 | NC_003143 NC_005810

93342 100271 | 95097 102026 | 6930 6930 | 99.99 | NC_003143 NC_005810

100260 105578 | 102955 108271 | 5319 5317 | 99.4 | NC_003143 NC_005810

In the dialog, user got to choose the query

genome and reference genome in the combo

boxes. See the sample file above, the

coordinates in [S1] and [E1] are counted in the

query genome, while the coordinates in [S2]

and [E2] are counted in the reference genome.

Append > Genome

Comparison > Mauve

Use this command to append a whole genome

alignment result generated by Mauve. The file

ends with “.backbone” which Mauve

generated during alignment. Use the Up and

Down buttons to rearrange the order of existed

genomes to match the order in your backbone

file, or the Remove button to remove a

genome from the list.

Pie Selection

One of the new features in 3D Genome Tuner

is giving demonstrations. When discussing

interesting regions on the genome, showing

them on the map will be a good idea. The pies

provide coverage of all features from the start

of the region to the end. User can easily

identify what changes take place in these

regions.

Use this command to a dialog prompting for

the begin position and end position of the pie,

which can be inputted in the edits or drag in

the slider controls. The genome map to be

attached should be selected in the combo box.

Color and alpha control the appearance of the

pie.


Reveal Hotspots

One of the new features in 3D Genome Tuner

is detecting significant changes in statistical

data, including GC-content, CDS length, CDS

and RNA number per frame, gene coverage,

and visualizes on the map. To compare data,

3D Genome Tuner assumes they are in normal

distribution. Once all values are calculated,

values fall out of the Confidence Interval are

presented on the map. Tests carried on frames

are shown in pies and individual genes are

labeled besides their locations.

l Very high or low GC-content: This

option calculates the GC-content per one

kilo bases, the frames fall out of the

confidence interval are drawn in pies on

the map.

l Very long or short CDS: This option

calculates the length of every CDS; the

CDS whose length falls out of the

confidence interval is labeled on the map.

l Cluster of CDS genes: This option

divides the whole genome into 100

regions, the number of CDS are

calculated for each region, the regions

whose CDS count fall out of the


the map.

l Cluster of RNA genes: This option

divides the whole genome into 100

regions, the number of RNA are

calculated for each region, the regions

whose RNA count fall out of the


the map.

l Low gene coverage: This option divides

the whole genome into 100 regions, the

gene coverage (length of genes/total

length) are calculated for each region, the

regions whose gene coverage fall out of

the confidence interval are drawn in pies

on the map.

Settings and Preference

The general preference and CDS classification

settings can be accessed from Tools > Option

and Tools > CDS Classification. The Option

panel contains six tabs which are:

Layout

The Layout option tab provides settings for

the general appearance and colors of the maps.

The following options are on the Layout

option tab:

l Change: Set color for the selected ring,

colors of the CDS and RNA genes are set

in CDS and RNA pages.

l Hide/Show: Toggle display on the

selected ring.

l Up arrow: Swap the radius of the selected

ring with the former ring.

l Down arrow: Swap the radius of the

selected ring with the latter ring.


l Unit: Set units of the coordinates.

l Radius: Set the radius of the selected

ring.

l Width: Set the width of the CDS, RNA or

Region ring.

l Background: Set background color for

the graph.

CDS

The CDS option tab provides settings for the

appearance and colors of CDS genes.

The following options are on the CDS option

tab:

l Use GO classification: Set color of CDS

genes using their COG category.

l Use COG classification: Set color of

CDS genes using their GO category.

l Length classification: Set color of CDS

genes in gradient colors according to

their length.

l Lines: Draw CDS in line which has a

fixed width.

l Polygons: Draw CDS in polygon whose

width reflects the length of CDS. CDS

gene drawn in polygon has width reflects

the length of the gene. However,

polygons cover up when too many CDS

genes and consume more CPU.

Alternatively, user could choose to draw

CDS in Line which has a fixed width.

Large genomes are with more than a

defined number of CDS genes use Line

mode automatically, this number can be

set in Options.

l Draw CDS in lines when CDS count is

more than #value: If the genome has

more than #value CDS genes, 3D

Genome Tuner automatically draw CDS

genes in lines.

l Strand sensitive: Draw the CDS genes on

forward strand and the genes on reverse

strand in separate rings.

RNA

The RNA option tab provides settings for the

appearance and colors of RNA genes.


Chart

The Chart option tab provides settings for the

appearance and colors of GC-content and

GC-skew charts.

The following options are on the Chart option

tab:

l Step: Set the proportions a genome will

be divided into. GC-content and

GC-skew are calculated on every

segment before drawing to the chart. The

change to this slider control only applies

on later sequences. The proportions range

from 10 to 1000 for GC-content and 100

to 10000 for GC-skew.

l Scale: Set extent for the chart.

l Alpha: Set alpha for the color of the chart,

The alpha ranges from 0 to 1.

BLAST

The BLAST option tab provides settings for

the appearance and colors of the orthologous

pairs. The Overlap measures the matching

length in the gene length (the longer between

query gene and reference gene). To specify the

color representing a certain overlap, user may

choose it in the dropdown lists.

l Matrix: choose the matrix when align

sequences with jaligner.

l Open Gap Penalty: choose the matrix

when align sequences with jaligner.

l Extend Gap Penalty: choose the matrix

when align sequences with jaligner.

l External BLAST Program Path: specify

the path of BLAST program when

aligning sequences.

l Alignment Colors: The colors of different

overlaps

Preference

l The System option tab provides settings

for the performance and profile of 3D

Genome Tuner.

l Auto save settings: Automatically save

settings on closing options sheet.

l Auto load settings: Automatically load

settings on starting the program.

l Enable anti-alias: Use anti-alias on the

lines and polygons.

l Direct connection: Connect to Internet

directly.

l Manual proxy configuration: Use proxy

to connect to Internet.

l Temporary Files: Specify a path where

temporary files during the runtime are

placed.

l Http proxy: Specify the address of the

proxy server when using Manual proxy

configuration

l Http proxy: Specify the port of the proxy

server when using Manual proxy

configuration.


CDS Classification Profiles

User can assign different colors to CDS genes

according to selected classification method.

The CDS Classification panel contains the

following tabs:

COG

Use Clusters of Orthologous Groups (COGs)

classification system to render CDS according

to its COG code, which can be obtained from

sequence alignment with COG databases. For

more detail on how to import COG

information, see Append > CDS Classification

GO

Use Gene Ontology (GO) classification

system to render CDS genes according to its

GO code. Currently, 3D Genome Tuner only

use the highest three levels for classifications.

For more detail on how to import COG

information, see Append > CDS Classification

Color Gradient

The color gradient classification method can

be applied when user wish to render CDS

genes in a gradient color according to their

length or GC-content. In this tab, the Start

Color means the color to fill minimal value

for the property, being whether length or

GC-content and End Color is for the

maximum value. The values in this range are

rendered in a gradient color which can be

divided in parts specified.

For more detail on how to set the canvas to

use gradient colors according to the properties

of CDS genes, see Options > CDS.


User Interface

Navigation Window

The navigation window allows you to quickly access features and statistics

of each genome. When mouse moves over an item in the tree control, a

tool tip which displays the detailed information of that item will show up.

The tool tip provides general information about the genome and counts for

CDS, RNA, etc. When mouse moves over an item representing a CDS or

RNA gene, the annotation of that gene will show up in the tool tip. Click

on that item and a label besides that gene in the map will show up. If you

click on an item in the “Orthologous Pairs”, a line linking the orthologous genes will appear in the

main graph.

Local Window

The local window shows an image of genes in a region between the begin position of the view

port of the main canvas and extends a length of 20kb of the selected genome which can be

changed in Genome Selector. The labels shown on the arrow lines are the locus tags of genes and

the colors of the arrow lines are the same as the colors which genes are rendered in the maps.


Chart Window

The chart window show the statistic charts in a region between the begin position in Edit1 and end

position in Edit2 in the sub-toolbar of all genomes. The genomes are differentiated by the vertexes

of the charts. The charts of GC-content, GC-skew and gene coverage can be found in the

following window:

Sequence Window

The sequence window shows the corresponding sequence and information of the selected gene in

the navigation window. The information of the gene includes locus_tag, begin position, end

position and product.

The right side of the window lists the annotation of the selected gene, with hyperlink associated to

its reference in the database.

Alignment Window

The alignment window shows the alignment of two genes of their amino acid sequences using

jaligner. The left side shows the similarity of every base and the right side shows a summary

report on this alignment.

Magnify Window

The magnify window is a larger version of the image of current view port in main canvas. This is

useful for those CDS genes are dense in the global view. On rotating to the left or right in the main

canvas, this magnified canvas rotates along with it.


Linear Chart Window

The command to show Linear Chart Window can be accessed from Tools > Linear Chart, this

window shows an image of linear genomic map of loaded sequences from their begin positions.

Use Move Left and Move Right buttons to navigate through the genomes. The Zoom In and

Zoom Out buttons are for scaling the image. The Rotate Angle button is useful when user wish to

have the captions of genes rotated a specific angle. At last, if the user wishes to export the image

for further use, press the Export Image button then choose a location to save the file.

Examples

In this section, several examples are provided to aid you on how to accomplish some basic

analysis using 3D Genome Tuner. The examples mentioned below use the sample files shipped

with the program, you can also download “samples.zip” file from the homepage. s

Import Sequence Files

This example shows how to import sequence files into 3D Genome Tuner:

Click File > Open, browse to “samples” directory, select AP009180.gb, AP009180.embl or

AP009180.fas then press the "OK" button.


Click File > Open Sequences, press the "Add" button, browse to “samples” directory, select

AP009180.gb, AP009180.embl orAP009180.fas then press the "OK" button.

Use the button Open Sequences on the toolbar, press the "Add" button, browse to “samples”

directory, select AP009180.gb/AP009180.embl/AP009180.fas then press the "OK" button.

Import CDS

This example shows how to import CDS genes to an existing genome.

First import a sequence file, see also Import sequences.

Click Append > CDS, browse to “samples” directory and select "CDS_Information_List.txt",

check the Has Title and Has COG box, change the edit of COG to 5, onward to the next page.

Change the radius and width if you feel like, as well as the Lines or Polygons, then press "Next".

In the last page, select Specify additional file and choose “CDS_Additional_Information.txt” or

leave it as default. See also the CDS menu command.

Import COG

This example shows how to set COG categories on the CDS genes of an existing genome.


If you import a FASTA format file, Import CDS before importing COG.

Click Append > COG, browse to “samples” directory and select “CDS_COG_Definition.txt”. Also

select the genome you would like to append COGs to, press the “OK” button. See also the COG

menu command.

Import regions

This example shows how to import regions and display them on an existing genome map.


Click Append > Region, browse to “samples” directory and select “regions.txt”, also select a

genome you would like to append regions to, onward to the next page. Change the radius and

width if you feel like, press the “Finish” button. See also the Region menu command.

Import BLAST

This example shows how to import BLAST output and link orthologous gene pairs between

genomes. .

First import at least two sequence files, see also Import sequences.

Make sure at least two genomes have CDS genes appended, if not, Import CDS before importing

BLAST.

Click Append > BLAST, browse to “samples” directory and select “BLAST.txt”, select the Query

Genome (which is the input when you ran BLAST program) and Reference Genome (which is the

database when you ran BLAST program) in the combo box, onward to the next page. Change the

display option if you feel like, press the “Finish” button. The links can be displayed by clicking

corresponding items in the navigation window. See also the BLAST menu command.


Import MUMmer

This example shows how to import NUCmer output and draw homologous regions on two

genomes.

First import at least two sequence files, see also Import sequences.

Click Append > MUMmer, browse to “samples” directory and select “NUCmer.coords”, select the

Query Genome (which is the first argv argument when you run NUCmer) and Reference Genome

(which is the second argument when you run NUCmer) in the combo box, press the “OK” button.

See also the MUMmer menu command.

Copyright

3D Genome Tuner is free software; you can redistribute it and/or modify it under the terms of the

Lesser GNU General Public License as published by the Free Software Foundation; either version

2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;

without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

PURPOSE. See the Lesser GNU General Public License for more details.

You should have received a copy of the Lesser GNU General Public License along with this

program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,

MA 02111-1307 USA

Contact

You may email any questions/suggestions to: [email protected]

You're welcome to report bugs at 3D Genome Tuner Discussion Forums.


3D Genome Tuner User Manual-2.1.0scape3d.sourceforge.net/3DGenomeTunerUserManual.pdf · 2011. 4. 26. · Open Files: Import one or more sequences into 3D Genome Tuner 3. Rotate Left:

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