3D Genome Tuner User Manual-2.1.0scape3d.sourceforge.net/3DGenomeTunerUserManual.pdf · 2011. 4....
Transcript of 3D Genome Tuner User Manual-2.1.0scape3d.sourceforge.net/3DGenomeTunerUserManual.pdf · 2011. 4....
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+
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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]
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
==================================================================================
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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
confidence interval are drawn in pies on
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
confidence interval are drawn in pies on
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
First import a sequence file, see also Import sequences.
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.
First import a sequence file, see also Import sequences.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.
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.
Generated by Foxit PDF Creator © Foxit Softwarehttp://www.foxitsoftware.com For evaluation only.