The 3D feature has not been tested with Release v5; however, it should still work.
Release: v5.1.0 (12June22)
The documentation has been moved from www.agcol.arizona.edu/software/symap to csoderlund.github.io/SyMAP.
Release: v5.0.8 (1June22)
- A new option "Concat" has been added; when this is unchecked, it will not create a
concatenation of the first genome to run against all chromosomes of the second, instead
it perform a chromosome-by-chromosome search.
- MUMmer4 can be used by compiling it on your machine from the /ext directory
and adding its path to the "symap.config" file. See Running MUMmer.
- When computing alignment&synteny, all stacktrace errors are now written into error.log.
- The database name is prefixed to the "logs/LOAD.log" file name.
- A new document has been created for when there is problems running
MUMmer from SyMAP.
- ConvertNCBI script was writing the scaffold sequences to end of the last chromosome (this
did not make the annotation or synteny wrong - just extra sequence).
Release: v5.0.7 (4Feb22)
- MUMmer has been updated since the last SyMAP release; the code in the /ext/mummer4 directory
has been updated for the latest MUMmer. The documentation has been updated accordingly
(see Running MUMmer).
- ConvertNCBI: (1) Include ncbi_dataset format. (2) Convert hex to character.
- Parameters: (1) The Load would not work if any numeric parameter was set to blank.
(2) For Alignment&Synteny "Parameters", the Global button was removed as it did not work
except under weird conditions.
- Help: the viewer Help pages link to the pages at www.agcol.arizona.edu/software/symap. The
approach for Mac was becoming obsolete, so it was changed. For Linux, more supported browsers were added.
- Improve documentation.
- Developers: Removed all Applet code (was disabled previously, but code was in everything).
Release: v5.0.6 (2June20)
- Some changes were necessary for SyMAP to run with MySQL v8.
- The schema needed a change, which will occur on first reading of database.
- SyMAP works on MacOS Catalina 10.15
- SyMAP can be compiled with Java v14 (some changed were necessary for this).
- The Applet has been removed and will no longer be supported. (It is in earlier SyMAP versions, and can
be obtained at github).
- The built-in MySQL database on Linux is no longer supported.
- The Alignment&Synteny has a couple checks for 'ordered_against' before processing:
(1) Is the order_against the same as the other selected project.
(2) Does the ordered directory already exist.
Release: v5.0.5 (2May20)
- Ordering algorithm: The main change is a rewrite of the ordering algorithm, which orders draft contigs
against a completed sequence closely related genome. The previous algorithm sometimes
would put many of the placed contigs incorrectly into 'chrUNK', though the
ordering in the anchored.csv file was correct.
- SyMAP Manager:
- Show #genes and #gaps in summary
- Add Project: On Linux, the "Add" button would stay disabled, this has been fixed.
- Chromosome Explorer: Mouse over a hit and the block number will be shown along with the other information.
- SyMAP Query:
The "Align Sequence" display now show locations in text box under alignment.
The v5.0.4 introduced a bug where the row selections display were not right, which
is fixed.
- Small changes:
- Running 'symap -v' will check the MySQL variables needed to run at a reasonable speed,
and will output to terminal any variables that need changing.
- Block View: When viewing the blocks using VNC, the chromosome that the
blocks were aligned to was not visible, which has been fixed.
- All Pairs button: Is only enabled if there is anything that will be executed when selected.
- Load Project: If a file of 100's of draft sequences are loaded, this was flagged as an error (but
still loaded); it no longer called an error, though a message is written to terminal.
Release: v5.0.4 (18Apr20)
- SyMAP Query has had major changes:
- It is faster, e.g. finding the hits in synteny blocks for 5 plant genomes did take 9m:32s
and now takes 0m:09s.
- The query page has changed to allow more versatile queries.
- The PgeneF is only computed if the "Compute PgeneF" option is checked; otherwise, there
is no changes to this function or options.
- Some of many minor changes:
- Selecting a chromosome for a species (or multiples) now only shows hits that involve the
selected chromosomes.
- The #RGN column has been removed and a new "Has Gene" column has been added. Note, all species
with a gene overlapping the hit should have 'annotation', but this makes it easier to see in a glance.
Plus, if some genes do not have an ID or some other keyword, it can be confusing looking at the
annotation.
- The "Save for Reload" and "Reload Results" have been removed, as it is so much faster, this
does not seem necessary anymore.
- Both the Overview and Table Summary have small changes.
- scripts/ConvertNCBI has been updated to also create a gap file.
- scripts/symap.sql has been removed and the schema has been incorporated into the Java code.
- SyMAP Summary: Displays major parameters for projects that are not loaded.
- Chromosome Explorer 2D View: The mouse over provides location information in the "Instruction" box,
plus:
- The following functions can be applied to the selected region of a sequence track:
"Zoom All Tracks", "Zoom Selected Tracks", "Align (Max 30000)", "Show Sequence", where the
first three are not new, but the labels changed for clarity.
- The last one, "Show Sequence", has
been added as there was no way to see the underlying sequence; it is simply a popup of the
selected sequence.
- The "Align" view has been slightly changed to add comma's in large numbers and the length of the sequence.
- The symapApplet.jar was not working in recent releases, which has been fixed.
Release: v5.0.3 (11mar20)
- Chromosome Explorer 2D view. The "Annotation Description" can be right-click to view
a pop-up of the description; the benefit is that sometimes part of the description is
buried, and the pop-up can be copied.
- SyMap Queries. (1) The filters set are shown at the top of the table. (2) The "Only
Orphan Genes" option can now only be used with the "Annotation Description", "Location", and
"Include" options.
- If access to MySQL does not work, a message is printed with the Java error message.
Release: v5.0.2 (24feb20)
- scripts/ConvertNCBI: (1) Produce a hard-masked genome sequence (input is soft-masked) with
-m flag. (2) Includes the mRNA ID in the product attribute. (3) The product attribute has
been improved.
- SyMAP Bug fix for using chromosome and scaffolds in the same project.
The following did not work:
Say the genomic sequence input was a mix of chromosomes (prefix 'Chr')
and scaffolds (prefix 's'), and the Project parameters were prefix 'Chr' and minsize '10000',
where the minsize filtered out annotated scaffolds, SyMAP would quit if there was
annotation on filtered-out scaffolds; this has been fixed. Also, the documentation
was not correct for mixing sequence types (e.g. prefix 'Chr' and 's'); the Project parameter
'grp_prefix' should be set to blank.
Release: v5.0.1 (16feb20)
- Load Annotation
- In the Params interface for a project, the user can set what keywords from the
column 9 "Attributes" field of the gff file to load; this was not working correctly
and has now been fixed.
- The type (column 3) of mRNA was being loaded as a gene, which causes duplicate records;
now mRNA's are ignored.
- Alignment & Synteny
- Though it was not possible to make MUMmer v4 part of SyMAP, it is possible
to install MUMmer v4 in the /ext/mummer directory and it will work. Instructions
are provided in System Guide.
- The nucmer "--maxmatch" parameter was automatically used for self-synteny when
a sequence file was being compared with itself; this would result in an extremely
long execution time for large files (e.g. chromosomes). Consequently, this
parameter has been removed, but can now be set by the user in the "Parameter" interface.
- Pair Parameters: (1) The user can set parameters in "Self Args", which are only
used when a chromosome sequence is being compared to itself. (2) This interface
was very confusing as to when parameters were saved and what would be used;
this should be clearer now, and is explained in the "Help" for the Parameter interface.
- If only part of the alignments finished and it ended pre-maturely, when run again,
it will not redo any finished alignments.
- Internally, goobs of commented out code has been removed.
Release v5.0 (22jan20)
New projects cannot be added to v4.2 databases, but they can be queried (e.g. dotplot).
The significant change
is with the file structure for the data, where the old file structure will not
work with this new release as shown further under Directory structure.
- General
- Error messages (and stack traces) are written to error.log
- There was one symap script with various flags, now there is four symap scripts
with less flags, as follows:
Script | Build | View | Has 3D view
| ./symap | Yes | Yes | No
| ./symap3D | Yes | Yes | Yes
| ./viewSymap | No | Yes | No
| ./viewSymap | No | Yes | Yes
|
- The symap -c command line parameter can be used to
specify a configuration file other than 'symap.config'
- The Summary list of all selected projects has been enhanced.
- Query database
- The "Display for Selected Pair:" popup Summary is now available for self-synteny and FPC-Seq
- Build database
Release: Jan2018 (build 120)
Release date: 1/16/18 - updated ConvertNCBI.java script.
Release date: 1/10/18
- A few more improvements on the applet code.
- Renamed some functions to make them clearer and updated the help.
- Improved the Help on the parameters page.
- Fixed a rare memory bug (occured on a self-synteny; requires the database to be re-created).
- The Image button does not work for Java v9, so a popup tells the user.
- Added a Java script called ConvertNCBI.java, as documented in NCBI to SyMAP.
Release date: 12/28/17 (build 119)
- The applet code has been fixed to work better.
- The FPC to sequence block view had a bug that was fixed (though 'reverse' does not work).
Release date: 12/24/17 (build 118)
- There was a limit of 75 sequenced regions per genome, which the block view did not work after that.
The limit has been changed to 150 and a popup message occurs if that limit is passed.
A script (scripts/lenFasta.pl) is supplied to provided the sorted lengths, where you should set the
min_size parameter to the 150th length.
Release date: 11/7/17 (build 117)
- Fixed problem that prevented symap from running with new JDK v9.
Release date: 1/7/16 (build 116)
- Fix display sizing errors in circle view display
- Fix database error for long project names (max project name remains 40)
Version 4.2
Release date: 4/23/2014
New Features:
- New, unified web access applet interface. Now you can present a unified SyMAP web display of some or all
of the projects in your database using just one small HTML page (no CGI). Applet interfaces are also
available for each of the sub-functions (dotplot, circle view, etc.) enabling customized web displays.
Modified Features:
- The Explorer has been updated to be more usable for draft projects, i.e. when there are many
sequences that have not been ordered and anchored to pseudomolecules. Specifically, it will now show
up to 450 sequences, and to decrease clutter it shows only sequences that actually have a synteny block.
- The prior web system files have been removed, including the cgi and supporting perl modules.
- The circle view now draws all text labels horizontally, due to rendering problems
with rotated text on several platforms (most severely on Mac). The rotated text is still available through a
checkbox option.
It is no longer necessary to run the perl install script to install web functionality.
Version 4.1
Release date: 2/20/2014
New Features:
- Publication-quality image saving. A save button has been added to every graphical window allowing saving to
a wide variety of formats, including scalable vector formats (svg, eps, pdf) which may be resized clearly to any size. (Many thanks to the developers of the FreeHEP Vector Graphics library, and especially Mark Donszelmann, for making this possible!)
- Download of block co-ordinates. Choose the species of interest, open the Explorer, and the download button is at the lower left.
Modified Features:
- Applet is signed with a DigiCert certificate, removing the security blocks which have been increasing
in recent Java versions.
- MUMmer binaries for Mac OSX have been replaced by 64-bit versions. The 32-bit versions which had been
supplied could not access more than 2G RAM, preventing alignment of many chromosomes.
Version 4.0
Release date: 7/15/2012
New Features:
- Project Manager Enhancements
- Create new projects through the Manager
- No need to create directories or copy files
- Alignment & Synteny parameters also available
- Query Page Enhancements
- Compute putative gene families across species
- Many additional filters
- Create and view Muscle multiple-alignment for selected results
- Additional Features
- Script 3track_figure.pl makes 3-genome figure for publication (see online
Tour;
script added to 4.0 package post-release)
Modified Features:
- Write contig anchoring information to a file (order_against mode)
- No longer creates the "_ordered" project output from order_against
- grp_prefix parameter now optional (but recommended). grp_sort eliminated.
- Self-alignments improved by using -maxmatch option of MUMmer for individual chromsome self-alignments
- Top-2 filtering modified to accept also hits within 80% of the 2nd best score, in order to
retain gene-family hits and allow identification of families through the query interface.
Version 3.5
Release date: 1/24/12
New Features:
- Dynamic circular display
- Circular-style view allowing addition/removal of species and chromosomes
- Replaces 3D view in the web applet (removing problems of MacOS support for 3D)
- 3D still available in standalone mode
- Annotation query interface (Java-based, upgrades the web CGI version)
- Project parameters editing window
- Unsigned web applet (no approval popups, if database and webserver have same host)
- For draft sequence using order_against, create ordered and anchored versions of the project
Modified Features:
- Added contig-flipping to draft sequence order_against function
- Added draft sequence ordering demo
- Improved command-line launch script
Version 3.4
Release date: 12/14/10
Modified Features:
- Query files catenated before running MUMmer, for substantial increase in speed.
- Batch alignment buttons added to Project Manager.
- Improvements to handling of unordered scaffolds, including:
- Scaffolds can all be in one fasta file.
- Added min_size parameter, to specify minimum size scaffold to load.
- Added order_against parameter, to specify reference sequence for ordering scaffolds
(the order only affects the dotplot display)
- Minor changes to CGI page displays to better accomodate unordered.
- Fix compilation error in 64-bit MUMmer binary, which prevented use of very long pseudomolecules.
Version 3.3
Release date: 10/4/10
Modified Features:
- Added "no_overlapping_blocks" parameter
- Added printout of block and synteny anchor tables to "/results" directory
- Remove "Contig0" (singleton clones) from FPC displays
- Adjustments to unannotated sequence clustering to obtain larger clusters,
not dependent on the order of scanning of MUMmer output files.
- When clicking a block in the dot plot, 2D view will open with hit filter setting "show only synteny hits"
- Some bug-fixes to search.cgi
Version 3.2
Release date: 6/9/10
Modified Features:
- Inversions are shown on the 3D view in green, where un-inverted are shown in red.
- Anchor chains are not merged.
- The dot plot background is white and the synteny blocks blue.
- SyMAP automatically only uses one processor unless specified otherwise with the -p option.
- The whole genome dot plot is available from the project manager.
- When running an alignment, a summary is listed to the terminal and to a log file.
- A lot of error checking has been added. However, every platform can have variations, which
we may not have accounted for. So PLEASE, let us know if you have any problems and we will
work with you to it.
Version 3.1
Release date: 2/12/10
This release includes major enhancements to the Dot Plot view.
New Features:
- Multi-genome Dot Plot: multiple species can be displayed on the y-axis against a common reference species.
- Dot Plot view integrated into 3D viewer, now the species/chromosomes displayed in the Dot Plot can be changed on-the-fly.
- Dot Plot reference species on the x-axis can be changed dynamically via a new drop-down menu.
- Main web page redesigned.
Version 3.0
Release date: 1/7/10
This major release includes many new features, in particular the 3D viewer and Project Manager.
New Features in User Interface:
- Multi-genome 3D viewer.
- Circular CGI view.
- Gene search CGI.
- Support for sequence-to-sequence alignment.
-
- Option to flip sequence.
- Zoom into sequence or hit regions using the mouse scroll wheel.
- Three-track CGI blocks view.
- Improved annotation display and addition of URL-embedding capability.
New Features in Back-End Processing:
- Completely rewritten in Java with major performance improvement.
- Addition of Project Manager GUI to simplify and automate back-end processing, sequence alignment, and synteny analysis.
- Support for sequence-to-sequence alignment.
-
- Hits are now clustered based on gene annotation and drawn as "ribbons" to indicate locations of sub-blocks.
Version 2.0
Release date: 5/18/07
This release includes many new features for the alignment view. The dot plot view was
not changed.
New Features Block view (CGI):
- View reverse option: reverse which of the two genomes is the reference genome.
- Chromosome view: the blocks are color coded to indicate which chromosome they are from. Also, the number of anchors is displayed over each block.
New Features on Java interface:
- Filters:
- For a given track (Block, Hit, Sequence) hover the mouse over the track and
right click. A menu of the most common filters is shown;
this is much easier than opening up the Filter window.
- From this window, you can go directly to the help for the given track.
There is also a 'Navigation Help', as there are many ways to resize, scroll, etc.
- Sequence track:
- Show hit score bar is a new filter that
shows the hits down the length of the sequence as a histogram showing how strong each hit is.
- Show Hit Score Value is a new filter that shows the %identity.
Note that the sequence graphic is twice as wide to show the score bar and score value.
- The sequence track can be scrolled by moving the mouse wheel when the
mouse is position over the sequence track.
This retains the same zoom and filters, but moves up or down the lenght of the sequence (i.e. pseudomolecule).
- The gene annotation now shows the intron/exon structure.
- Hit track:
- Show Only Gene Hits (contained) is a new filter that turns off the
display of all hits unless they are contained in an annotated gene.
- Show Only Gene Hits (overlap) is a new filter that turns off the
display of all hits unless they overlap an annotated gene (but is not contained in a gene).
- Show Only Non-Gene is a new filter that turns off the
display of all hits unless they are NOT overlapping or contained in a gene.
- Hit lines are highlighted in red when mouse positioned over a hit.
- Block track:
- When hovering over a contig, the contig information at the bottom of the
display includes all the chromosomes that the contig hits.
- Bug Fixes:
- Genes drawn incorrectly when sequence range within gene boundary.
- Fixed bug with pseudomolecule filter.
- Certain queries were failing when used with MySQL 5.0.26 due to comma precedence change.
New Features in Back-End Processing:
- Support for mixed letter/number chromosome names and arbitrary ordering (see example in demo-fpc params file)
- Pseudomolecule sequences loaded in 1Mb chunks, removing database problems with large text fields
- Filtering optimized in anchors.pl to reduce memory use in loading large blat outputs
Version 1.0
Release date: 9/1/06
First full public release.
Email:
symap@agcol.arizona.edu
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