The ACT Manual

 

Copyright © 2000-2019 by Genome Research Limited

 

This document describes ACT - a DNA sequence comparison viewer included as part of release 18 of the Artemis tool set.

 

ACT is free software; you can redistribute it and/or modify it under the terms of the 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 GNU General Public License for more details.

 

You should have received a copy of the 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

 

For the full text of the license see the section called Copyright Notice in Chapter 1 .

 

 

 

 

Table of Contents

 

Chapter 1. Introduction to ACT  1

What is ACT?   1

System Requirements   1

Getting and Installing ACT   1

Installing Java   1

Installation Instructions for UNIX and GNU/Linux   1

Installation Instructions for MacOSX   1

Installation Instructions for Windows   1

Concepts   1

The "Entry"   1

EMBL/Genbank Features   1

EMBL/Genbank Feature Keys   1

EMBL/Genbank Feature Qualifiers   1

"Tab" Files or "Table" Files   1

The Active Entries   1

The Default Entry   1

Feature Segments   1

The Selection   1

Feature Colours   1

Contributions and Suggestions   1

Distribution Conditions and Acknowledgments   1

Copyright Notice   1

Chapter 2. Starting ACT  1

Running a Comparison   1

The MSPcrunch Comparison File Format  1

Running ACT on UNIX and GNU/Linux Systems   1

UNIX Command Line Arguments for ACT   1

-options   1

-Xmsn -Xmxn   1

-Dblack_belt_mode=false   1

-Doffset=10000   1

-Duserplot=pathToFile   1

-Dloguserplot=pathToFile   1

-Dbam1=pathToFile1 -Dbam2=pathToFile2   1

-Dshow_snps   1

-Dshow_snp_plot  1

-Dshow_cov_plot  1

-Dchado="hostname:port/database?username"   1

-Dread_only   1

-Dshow_forward_lines=false   1

-Dshow_reverse_lines=false   1

Running ACT on Macintosh Systems   1

Running ACT on Windows Systems   1

The ACT Launch Window     1

The File Menu   1

Open ...  1

Quit  1

The Options Menu   1

Re-read Options   1

Enable Direct Editing   1

Genetic Code Tables   1

Send Searches Via SSH    1

Black Belt Mode   1

Highlight Active Entry   1

Show Log Window     1

Hide Log Window     1

Chapter 3. The ACT Main Window   1

Overview of the Comparison Window     1

The File Menu   1

Read An Entry ...  1

Save Entry   1

Save All  1

Write   1

Amino Acids Of Selected Features   1

PIR Database Of Selected Features   1

Bases Of Selection   1

Upstream Bases Of Selection   1

Downstream Bases Of Selection   1

All Bases   1

Codon Usage of Selected Features   1

Read BAM / CRAM / VCF ...  1

Edit In Artemis ...  1

Close   1

The Entries Menu   1

Set Name Of Entry   1

Set Default Entry   1

Remove An Entry   1

Remove Active Entries   1

Deactivate All Entries   1

The Select Menu   1

Feature Selector ...  1

All  1

All Bases   1

Select All Features in Non-matching Regions   1

None   1

By Key   1

CDS Features   1

Same Key   1

Open Reading Frame   1

Features Overlapping Selection   1

Features Within Selection   1

Base Range ...  1

Feature AA Range ...  1

Toggle Selection   1

The View Menu   1

Selected Features   1

Selection   1

Search Results   1

CDS Genes And Products   1

Feature Filters   1

Suspicious Start Codons ...  1

Suspicious Stop Codons ...  1

Non EMBL Keys ...  1

Duplicated Features ...  1

Overlapping CDS Features ...  1

Features Missing Required Qualifiers ...  1

Filter By Key ...  1

Selected Features ...  1

Overview     1

Sequence Statistics   1

Feature Statistics   1

Forward Strand Overview     1

Reverse Strand Overview     1

Feature Bases   1

Feature Bases As FASTA    1

Feature Amino Acids   1

Feature Amino Acids As FASTA    1

Feature Statistics   1

Feature Plots   1

Adjust panel heights ...  1

The Goto Menu   1

Navigator ...  1

Start of Selection   1

End of Selection   1

Feature Start  1

Feature End   1

Start of Sequence   1

End of Sequence   1

Feature Base Position ...  1

Feature Amino Acid ...  1

The Edit Menu   1

Undo   1

Redo   1

Selected Features in Editor  1

Subsequence (and Features)  1

Find Or Replace Qualifier Text  1

Qualifier(s) of Selected Feature   1

Change ...  1

Remove ...  1

Convert ...  1

Selected Feature(s)  1

Duplicate   1

Merge   1

Unmerge   1

Unmerge All Segments   1

Delete   1

Delete Exons   1

Remove Introns   1

Move Selected Features To   1

Copy Selected Features To   1

Trim Selected Features   1

To Met  1

To Any   1

To Next Met  1

To Next Any   1

Extend Selected Features   1

To Previous Stop Codon   1

To Next Stop Codon   1

To Next Stop Codon and Fix   1

Fix Stop Codons   1

Automatically Create Gene Names   1

Fix Gene Names   1

Bases   1

Reverse And Complement  1

Reverse And Complement Selected Contig   1

Delete Selected Bases   1

Add Bases At Selection   1

Add Bases From File ...  1

Replace Bases At Selection   1

Contig Reordering ...  1

Header Of Default Entry   1

The Create Menu   1

New Feature   1

Feature From Base Range   1

Intergenic Features   1

Features From Non-matching Regions   1

New Entry   1

Mark Open Reading Frames ...  1

Mark Empty ORFs ...  1

Mark Open Reading Frames In Range ...  1

Mark From Pattern ...  1

Table 3-1. IUB Base Codes   1

Mark Ambiguities   1

The Run Menu   1

Configuring the Run Menu   1

The Graph Menu   1

Hide All Graphs   1

Add Usage Plots ...  1

Add User Plot ...  1

GC Content (%)  1

GC Content (%) With 2.5 SD Cutoff  1

AG Content (%)  1

GC Frame Plot  1

Correlation Scores   1

Reverse Correlation Scores   1

GC Deviation (G-C)/(G+C)  1

AT Deviation (A-T)/(A+T)  1

Karlin Signature Difference   1

Cumulative AT Skew and Cumulative GC Skew     1

Positional Asymmetry   1

Informational Entropy   1

Scaled Chi Square   1

Mutational Response Index   1

Effective Codon Number  1

Intrinsic Codon Deviation Index   1

The Display Menu   1

Hide Frame Lines   1

Show Frame Lines   1

The DNA Views   1

Changing the Selection from a View Window     1

Other Mouse Controlled Functions   1

The Pop-up Menu   1

Pop-up Menu Functions   1

Toggle Buttons   1

Feature Labels   1

One Line Per Entry   1

Forward Frame Lines   1

Reverse Frame Lines   1

Start Codons   1

Stop Codons   1

Feature Arrows   1

Feature Borders   1

All Features On Frame Lines   1

Flip Display   1

Colourise Bases   1

Scrolling The View     1

Changing The Scale   1

"Direct Editing"   1

Comparison View     1

Controls   1

The Comparison View Pop-up Menu   1

The Feature List  1

Changing the Selection from the Feature List  1

Other Mouse Controlled Functions   1

The Pop-up Menu   1

Save List to File   1

Show Selected Qualifier  1

Show Correlation Scores   1

Show Gene Names   1

Show Qualifiers   1

Show Product  1

Scrolling The List  1

Graphs and Plots   1

Notes on Using The Mouse   1

Chapter 4. Secure Shell (SSH) Plugin To ACT Overview of the SSH Plugin  1

Login In   1

Setting up a SSH tunnel  1

Using Putty to Set Up A Tunnel  1

Chapter 5. ACT Configuration Options  1

The Options File   1

ACT Option Descriptions   1

font_size   1

font_name   1

base_plot_height  1

feature_plot_height  1

draw_feature_borders   1

show_forward_lines   1

show_reverse_lines   1

draw_feature_arrows   1

overview_feature_labels   1

overview_one_line_per_entry   1

show_list  1

show_base_view     1

features_on_frame_lines   1

frame_line_features   1

feature_labels   1

one_line_per_entry   1

genetic_codes   1

translation_table_1   1

extra_keys   1

extra_qualifiers   1

common_keys   1

hyperlinks   1

undo_levels   1

minimum_orf_size   1

direct_edit  1

feature_dna_programs   1

feature_protein_programs   1

ncbi_dna_search   1

ncbi_protein_search   1

Setting Colours   1

Options For Plots and Graphs   1

Options For A Chado Database   1

chado_exon_model  1

chado_transcript  1

chado_servers   1

Options File Format  1

An Example Options File   1

 

List of Tables

 

3-1. IUB Base Codes

 

 

 


 

Chapter 1. Introduction to ACT

 

What is ACT?

 

 

ACT is a DNA sequence comparison viewer based on Artemis. The name ACT stands for Artemis Comparison Tool. ACT is written in Java, reads EMBL or GENBANK format sequences and feature tables, and can work on sequences of any size.

 

ACT understands several different comparison file formats. See the section called Running a Comparison in Chapter 2 for details. Note that ACT is a comparison viewer only. The comparison information itself must be generated externally. See the section called Running a Comparison in Chapter 2 for more details.

 

For other information see the ACT web pages or the Artemis web pages.

 

 

 

System Requirements

 

ACT will run on any machine that has a recent version of Java. This version of ACT requires Java 9 at least and preferably Java 11. See the section called Getting and Installing ACT for details on how to get Java.

 

 

 

 

Getting and Installing ACT

 

ACT is included in the Artemis tool set package. The most up to date version of ACT is always available from the ACT web pages.

It’s also available bundled with Java from Bioconda for Mac OSX or UNIX based systems.

 

 

Installing Java

 

Before installing Artemis you will need to make sure you have Java installed. The previous v17.0.1 version of Artemis required Java 1.8 to run. All subsequent recent versions from v18.0.0 onwards require a minimum of Java 9 and preferably Java 11.

 

The licensing for Java has recently changed and Oracle now offers two flavours – one free GPL licensed GA OpenJDK and one commercial build that requires a subscription for production use. The default option should be the OpenJDK, but this choice may be dependent upon your organisation so check with your administrator if necessary.

There are a number of ways to install the open JDK Java. The easiest is via the AdoptOpenJDK web site - just select the OpenJDK version and Hotspot options for the relevant platform and you’re done.

Other options include Homebrew for Mac OSX or apt on Linux. The current Java 11 version can always be obtained from https://jdk.java.net/archive/. Select the relevant download link for your operating system, from the Build section of the page. You will generally need administrator privileges for your machine, to successfully install Java.

The download files are either .tar.gz or .zip archives, dependent on operating system. Double-clicking on the downloaded file will usually extract the contents. They may also be extracted on the command line using

$ tar xvf openjdk-11*_bin.tar.gz

or

$ unzip openjdk-11*_bin.zip

The uncompressed folder will be named similar to jdk-VersionNumber.jdk, e.g. jdk-11.0.1.jdk.

Some good advice on installation can be found in the following articles:

For Ubuntu:    https://linuxize.com/post/install-java-on-ubuntu-18-04/

                        https://dzone.com/articles/installing-openjdk-11-on-ubuntu-1804-for-real

For Mac OS X: https://stackoverflow.com/questions/52524112/how-do-i-install-java-11-on-mac-osx-allowing-version-switching

For Windows: See the first answer in https://stackoverflow.com/questions/52511778/how-to-install-openjdk-11-on-windows

Typically:

·      For Linux, copy the uncompressed folder into /usr/lib/jvm. Alternatively, use apt or similar, for example:

sudo apt update

sudo apt install default-jdk

java -version

·      For Macs, you will need to copy the uncompressed folder to your /Library/Java/JavaVirtualMachines/ folder since this is the standard location for Java installs, and add the following to your profile (e.g. .bashrc file):

export JAVA_HOME=”/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home”

export PATH="$JAVA_HOME/bin:$PATH"

·      For Windows, make a new “Java” folder under C:\Program Files and copy the uncompressed folder into it. Now Create a new JAVA_HOME environment variable using the Windows Control Panel “System” program. Set it to the path of your newly installed Java folder, e.g. C:\Program Files\Java\jdk-11.0.1.jdk. Now edit the PATH environment variable value and add %JAVA_HOME%\bin: to the start of it. You should now be able to bring up a DOS cmd window and run “java -version” in it, which should show the correct version, e.g. Java 11.

 

 

 

 

Installation Instructions for UNIX and GNU/Linux

 

Change directory to the directory you wish to install the Artemis software in. We will use ~/ in this example and in the next chapter.

 

Uncompress and untar the artemis-unix-release-{version}.tar.gz or artemis-unix-release-{version}.zip file. On UNIX the command for the v18.0.0 release would be:

 

tar zxf artemis-unix-release-18.0.0.tar.gz

 

This will create a directory called ~/artemis which will contain all the files necessary for running Artemis, ACT and associated tools.

 

For instructions on how to run ACT on UNIX and GNU/Linux once the archive is unpacked see the section called Running ACT on UNIX and GNU/Linux Systems in Chapter 2.

 

 

 

 

Installation Instructions for MacOSX

 

For MacOSX users, an archive artemis-macosx-release-{version}.dmg.gz disk image is provided. Your Mac may uncompress this automatically on download. If not it can be uncompressed by double-clicking on it or by using gunzip, e.g. for the v18.0.0 release:

 

gunzip artemis-macosx-release-18.0.0.dmg.gz

 

Alternatively, try the StuffIt Expander app. Double-click on any file ending in ".gz" and StuffIt Expander will be launched to uncompress that file.

 

The uncompressed disk image file artemis-macosx-release-{version}.dmg can be mounted by double clicking on it. The mounted image, "Artemis_Tools", can then be opened and the software contents displayed by clicking on it.

 

There’s also an artemis-macosx-chado-release-{version}.dmg disk image that will start up ACT with Chado connectivity, if you wish to work connected to a Chado database. This is installed in exactly the same way.

 

For instructions on how to run ACT on Windows once it is unpacked see the section called Running ACT on Macintosh Systems in Chapter 2.

 

 

 

Installation Instructions for Windows

 

On Windows systems, installing ACT is as simple as downloading the artemis-windows-release-18.0.0.zip file to an appropriate place (such as the desktop or the Programs folder).  Unzip the file using WinZip or equivalent. The unzipped folder will contain the Artemis tool set executable .jar files.

 

For instructions on how to run ACT on Windows once it is unpacked see the section called Running ACT on Windows Systems in Chapter 2.

 

 

 

 

Concepts

 

Here are some general concepts about ACT that may make the rest of this manual clearer.

 

 

 

 

The "Entry"

 

An "entry" in ACT-speak is not necessarily a complete EMBL or GENBANK entry. In most places in this manual when we refer to an entry we mean a file that contains just the feature table lines (the FT lines) of an EMBL/GENBANK entry (see the section called "Tab" Files or "Table" Files). After loading a sequence and opening an entry edit window (see  it is then possible to overlay many feature tables (see the section called Read An Entry ... in Chapter 3). Each of these feature table files is called an entry by ACT and it's features are kept separate from those of other entries.

 

This meaning of the word "entry" is used by most of the items in the File menu (see the section called The File Menu in Chapter 3) and by the items in the Entry menu (see the section called The Entries Menu in Chapter 3).

 

 

 

 

EMBL/Genbank Features

 

A "feature" in an EMBL or Genbank file is a region of DNA that has been annotated with a key/type (see the section called EMBL/Genbank Feature Keys) and zero or more qualifiers (see the section called EMBL/Genbank Feature Qualifiers). In an EMBL or Genbank formatted file the features of a piece of DNA are listed in the feature table section (see the section called "Tab" Files or "Table" Files).

 

 

 

 

 

EMBL/Genbank Feature Keys

 

All EMBL and Genbank features have exactly one "key" assigned to them. The key is the type of the feature. Examples include CDS (a CoDing Sequence), intron and misc_feature (MISCellaneous

 

feature).

 

The EBI has a list of all possible feature keys.

 

 

 

EMBL/Genbank Feature Qualifiers

 

The qualifiers of a feature in an EMBL or Genbank file are the notes and extra information about the feature. For example an exon feature might have a /gene="ratC" qualifier, meaning that the exon feature is part of a gene named ratC.

 

The EBI has a list of all possible feature qualifiers.

 

 

 

 

"Tab" Files or "Table" Files

 

An EMBL or Genbank file that only contains a feature table (just FT lines, no sequence or header lines) is called a "table" file, or sometimes just a "tab" file because the often has a name like "somefile.tab".

 

 

 

 

The Active Entries

 

All entries in ACT are considered to be "active" or "inactive". The overview, DNA view and feature list parts of the main window will only display features from active entries. To find out how to set the active and inactive entries see the section called The Entries Menu in Chapter 3.

 

 

 

 

The Default Entry

 

Many actions (such as creating features) require an entry to be identified as the source or destination for the action. Some actions, such as "Move Selected Features To ..." in the edit menu, will explicitly ask for an entry, but some assume that the action refers to a "default entry" that was previously set by the user.

 

The default entry can be set by using the "Set Default Entry ..." menu item in the Entries menu (see the section called Set Default Entry in Chapter 3).

 

 

 

 

Feature Segments

 

The term "segment" in the context of a CDS feature means "exon". We use the term "segment", because non-CDS features (such as misc_feature) can have exon-like parts too, but the term "exon" would be inappropriate in that case.

 

 

 

 

The Selection

 

In common with applications like word processors and graphics programs, ACT allows the user to "select" the objects that the program will act on. The objects to act on in ACT are features, feature segments or bases. If a feature segment is added to the selection, the feature that contains the segment is implicitly added as well. The current selection can be changed with the Select Menu (see the section called The Select Menu in Chapter 3) or using the mouse (see the section called Changing the Selection from a View Window in Chapter 3).

 

 

 

 

Feature Colours

 

Each feature displayed in ACT can be given a colour. The available colours are set in the options file (see Chapter 5) and are assigned to a feature by adding a /colour qualifier (see the section called Selected Features in Editor in Chapter 3). Currently there are two ways of specifying feature colours. The first way uses a single number. For example red is colour 2, so adding /colour=2 as a feature qualifier will make that feature red. The second way is to specify the red, green and blue components of the colour. Each of the components can take values from 0 to 255, with 255 being the most intense. For example /colour=255 0 0 is another way to give a feature the colour red. If no /colour qualifier is set for a feature a default colour is used (the default colours are also specified in the options file).

 

 

 

 

Contributions and Suggestions

 

We welcome contributions to ACT and to Artemis, bug reports from users and suggestions for new features. An email discussion list has been set up for this purpose. To join, send a message to 'artemis-users-join@sanger.ac.uk' with 'subscribe artemis-users' in the body (not the subject). Announcements will also be sent to this list.

 

 

 

 

Distribution Conditions and Acknowledgments

 

ACT may be freely distributed under the terms of the GNU General Public License. See the section called Copyright Notice for the full text of the license.

 

The development of ACT is funded by the Wellcome Trust through its support of the Pathogen Informatics Group at The Sanger Institute.

 

 

 

 


Copyright Notice

 

GNU GENERAL PUBLIC LICENSE

Version 2, June 1991

 

Copyright (C) 1989, 1991 Free Software Foundation, Inc.

 

59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

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Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations.

 

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The precise terms and conditions for copying, distribution and modification follow.

 

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7.  If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program.

 

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This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.

 

8.  If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License.

 

9.  The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.

 

Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.

 

10.  If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally.

 

NO WARRANTY

 

11.  BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

 

12.  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

 

 

 

 


 

Chapter 2. Starting ACT

 

 

Running a Comparison

 

Before running ACT you will need to obtain a comparison file. ACT comparison files can be created in a number of ways:

 

     Using the NCBI Blast website tblastx/blastn pages. This is the simplest method. Two fasta files can be uploaded and compared. A comparison file is generated that can then be downloaded in “hit table” format.

 

     Using the output of  BLAST version 2.2.2 or better. The blastall command must be run with the -m 8 flag which generates one line of information per HSP. If BLAST+ is used then the legacy_blast.pl PERL script (bundled along with the BLAST+ applications) can be used to generate the tabular format or run it with the -outfmt 6 flag. For more details see the BLAST+ manual.

 

     MEGABLAST output. ACT can also read the output of MEGABLAST, which is part of the blast+ distribution.

 

     MSPcrunch output. MSPcrunch is program for UNIX and GNU/Linux systems which can post-process BLAST version 1 output into an easier to read format. MSPcrunch much be run with the -d flag.

 

 

 

 

 

 

The MSPcrunch Comparison File Format

 

Here is an example input file generated by MSPcrunch -d.

 

1399    97.00   940      2539    sequence1.dna           1          1596    AF140550.seq

1033    93.00   9041    10501 sequence1.dna            9420    10880 AF140550.seq

828      95.00   6823    7890    sequence1.dna            7211    8276    AF140550.seq

773      94.00   2837    3841    sequence1.dna            2338    3342    AF140550.seq

 

The columns have the following meanings (in order): score, percent identity, match start in the query sequence, match end in the query sequence, query sequence name, subject sequence start, subject sequence end, subject sequence name.

 

The columns are separated by spaces.

 

 

 

 

Running ACT on UNIX and GNU/Linux Systems

 

On Unix and GNU/Linux the easiest way to run the program is to run the script called act in the ACT installation directory (see the section called Getting and Installing ACT) like this:

 

artemis/act

 

If all goes well you will be presented with a small window with one menu (the File menu). See the section called The ACT Launch Window for a description of this window.

 

Alternatively you start ACT with the names of two sequence/EMBL/GENBANK files and a file containing the comparison data eg:

 

artemis/act sequence1 blast_output.crunch sequence2

 

If you have more than two sequences (there is no upper limit) they should be listed on the command line separated by the corresponding comparison file:

 

artemis/act sequence1 seq2_v_seq1.crunch sequence2 seq3_v_seq2.crunch sequence3

 

See the section called UNIX Command Line Arguments for ACT or a list of the other possible command line arguments. Also to see a summary of the options type:

 

artemis/act -help

 

 

 

 

 

 

UNIX Command Line Arguments for ACT

 

As well as the listing file names on the command line, the following switches are available to UNIX users:

 

 

 

-options

 

This option instructs ACT to read an extra file of options after reading the standard options. (See the section called The Options File in Chapter 5 for more about the ACT options file.)

 

For example -options ./new_options will instruct ACT to read new_options in the current directory as an options file.

 

 

 

-Xmsn -Xmxn

 

Use -Xmsn to specify the initial size, in bytes, of the memory allocation pool. This value must be a multiple of 1024 greater than 1MB. Append the letter k or K to indicate kilobytes, or m or M to indicate megabytes.

 

Use -Xmxn to specify the maximum size, in bytes, of the memory allocation pool. This value must a multiple of 1024 greater than 2MB. Append the letter k or K to indicate kilobytes, or m or M to indicate megabytes.

 

 

 

-Dblack_belt_mode=false

 

If this is set to false then warning messages are kept to a minimum.

 

 

 

 

-Doffset=10000

 

This sets the base position that ACT opens at, e.g. 10000.

 

 

 

 

-Duserplot=pathToFile

 

This can be used to open userplots from the command line. The paths are comma separated to open multiple plots (-Duserplot='/pathToFile/userPlot1,/pathToFile/userPlot2').

 

In ACT numbers are used to associate the file with a particular sequence. For example to add a userplot to the second sequence:

 

act -Duserplot2=/pathToFile/userPlot

 

 

 

 

-Dloguserplot=pathToFile

 

This is the same as the above userplot option except that the log transform of the data is plotted.

 

 

 

 

-Dbam1=pathToFile1 -Dbam2=pathToFile2

 

This can be used to open BAM/CRAM files and/or VCF/BCF files (see the section called Read BAM / CRAM / VCF ... in Chapter 3 for more about the using these file types). This can take a path name to a file or an HTTP address. Numbers are used to associate the file with a particular sequence. For example to add a BAM to the first (top) sequence in ACT:

 

act -Dbam1=/pathToFile/file.bam

 

 

 

 

-Dshow_snps

 

Show SNP marks in BAM/CRAM panels.

 

 

 

 

-Dshow_snp_plot

 

Automatically open SNP plots for BAM/CRAM files that are opened.

 

 

 

 

-Dshow_cov_plot

 

Automatically open coverage plots for BAM/CRAM files that are opened.

 

 

 

 

-Dchado="hostname:port/database?username"

 

This is used to get ACT to look for the database. The address of the database (hostname, port and name) can be conveniently included (e.g. -Dchado="genedb-db.sanger.ac.uk:5432/snapshot?genedb_ro") and these details are then the default database address in the popup login window.

 

 

 

-Dread_only

 

For a read only chado connection -Dread_only is specified on the command line (e.g. art -Dchado="genedb-db.sanger.ac.uk:5432/snapshot?genedb_ro" -Dread_only).

 

 

 

-Dshow_forward_lines=false

 

Hide/show forward frame lines.

 

 

 

 

-Dshow_reverse_lines=false

 

Hide/show reverse frame lines.

 

 

 

 

Running ACT on Macintosh Systems

 

On MacOSX machines ACT can be started by double clicking on the ACT icon. The icon can be added to the dock by dragging it from a 'Finder' window and dropping it onto the position in the dock you want it.

 

To change the memory allocated to ACT on MacOSX, set the value in the file Info.plist in the directory ACT.app/Contents. Towards the bottom of the file you will see these lines:

 

<key>JVMOptions</key>

<array>

<string>-mx2g</string>

 

Changing the value after -mx will change the max memory used by Artemis. The default is 2Gb.

 

Similarly, to start ACT with a particular default Chado database connection you can add a <string>-Dchado=”connection string”</string> line to the above section (see -Dchado="hostname:port/database?username").

 

 

 

 

Running ACT on Windows Systems

 

On Windows, ACT can be started by double clicking on the act.jar icon, and similarly for the other tools.

 

If it fails to start, then it’s likely that either Java is not installed properly, or another program has hijacked the .jar file association (this could happen if a .jar was previously opened with Notepad for example, and then that association saved as the default). To check that Java is installed, run up a DOS window (Type cmd in the run menu) and then in the DOS window type java -version – this should display the correct Java version number.

 

To fix an incorrect file association, https://stackoverflow.com/questions/7325676/java-can-run-jar-from-cmd-but-not-by-double-clicking provides some helpful information.

 

A backstop solution that always works is to create a text file in Notepad [or an alias] with the following line in it:

 

java -jar act.jar

 

 

Save this file as act.bat in the same folder as the jar file (i.e. change the default .txt file extension to .bat before saving). Then just double click on that file instead of the .jar. The same can be done for the other tools.

 

 

 

 

The ACT Launch Window

 

This is the first window that opens when you start ACT.

 

 

 

 

The File Menu

 

Open ...

 

If you select this menu item a file requester will be displayed which allows you to open the sequence files and the comparison files. If the files you select are read successfully, a new window will open, which shows the sequences and the comparison. See Chapter 3 to find out how to use the main window. The comparison file is described in the section called The MSPcrunch Comparison File Format.

 

The "more files ..." button expands the window so that more sequence and comparison files can be read.

 

 

 

 

 

Quit

 

This menu item will close all windows and then exit the program

 

 

 

 

The Options Menu

 

Re-read Options

 

Choosing this menu item will discard the current options settings and then re-read the options file. Note that changing the font size in the file and then selecting this menu item will only change the font size for new windows, not existing windows. Currently some options are unaffected by this menu item. See the section clled Options File Format in Chapter 5 for more information about options.

 

 

 

 

 

Enable Direct Editing

 

This menu item will toggle "direct editing" option. It is off be default because it can have surprising results unless the user is expecting it. See the section called "Direct Editing" in Chapter 3 for more detail about this.

 

 

 

 

 

Genetic Code Tables

 

These options make all the NCBI Genetic Codes available. The default setting is the Standard Code. This setting effects the display of start codons (see the section called Start Codons in Chapter 3) and the "Suspicious Start Codons ..." feature filter (see the section called Suspicious Start Codons ... in Chapter 3).

 

 

 

 

 

Send Searches Via SSH

 

This is an advanced option for sites that have set up the ability to submit searches via SSH to another machine.

 

 

 

 

 

Black Belt Mode

 

This is an advanced option that can be used to turn off warning message. This options is displayed if the java property (black_belt_mode) is specified on opening up ACT, i.e. art -Dblack_belt_mode=yes.

 

 

 

 

 

Highlight Active Entry

 

When this option is on and the "One Line Per Entry" is on (see the section called One Line Per Entry in Chapter 3) the line that the active entry is on will be highlighted in yellow.

 

 

 

Show Log Window

 

Show the log of informational messages from ACT. Currently the log window is only used on UNIX and GNU/Linux systems to show the output of external programs. This menu item is only available when running ACT on UNIX or GNU/Linux systems. The logging is controlled by log4j. The log4j.properties file (etc/log4j.properties in the source distribution) sets the level of logging. This can be used to send the logging information to other places such as a file.

 

 

 

 

 

Hide Log Window

 

Hide the log of informational messages. This menu item is only available when running ACT on UNIX or GNU/Linux systems.

 

 

 

 


 

Chapter 3. The ACT Main Window

 

This chapter describes the main viewing window of ACT. First is an overview of the window and a description of the menus. The menus are also accessible from the pop-up menu in the view windows (see the section called Other Mouse Controlled Functions and the section called The Pop-up Menu for more).

 

 

 

 

Overview of the Comparison Window

 

The following images show a breakdown of the main ACT window taken from a screen shot of a two sequence comparison.

 

 

 

Key:

 

1.     The menus for the main window (described later in this chapter). Each menu contains a sub-menu to control each of the sequences in the comparison. The Display menu (see the section called The Display Menu) is the exception since it controls the overall display. Note that all the menus apart from the File menu and the Display menus can also be accessed via a pop-up menu on the third mouse button. See the section called Other Mouse Controlled Functions and the section called The Pop-up Menu for more.

 

2.     This a view of the subject sequence of the comparison. See the section called The DNA Views for more information on how to operate this part of the window.

 

3.     This part of the window shows the comparison between the two sequences. See the section called Comparison View for more information.

 

4.     The query sequence of the comparison. See the section called The DNA Views for more.

 

 

 

 

 

The File Menu

 

 

 

 

 

Read An Entry ...

 

Read an entry for this sequence, but keep it separate from the others. See the section called The "Entry" in Chapter 1 to see what we mean when we say "entry". The new entry will be marked as active (see the section called The Active Entries in Chapter 1) and will be the new default entry (see the section called The Default Entry in Chapter 1).

 

This function only reads the feature section of the input file - the sequence (if any) is ignored.

 

ACT can read these feature file formats:

 

     EMBL or GenBank feature tables

 

     GFF files

 

     Comparison file formats discussed in the Running a Comparison section.

 

 

 

 

 

Save Entry

 

Save the entry to the file it came from, unless the entry has been given a new name, in which case the entry is saved to a file with that name. If the entry has no name, ACT will prompt the user for a new name.

 

 

 

 

 

Save All

 

Save all the entries that have been loaded on top of this sequence.

 

 

 

Write

 

 

 

 

 

 

Amino Acids Of Selected Features

 

Prompt for a file name and then write the translation of the bases of the selected features to that file. The file is written in FASTA format.