Minor Updates to DNA Stacks v. 1.3

Eernisse, D.J. 2000. DNA Stacks: A software package for molecular systematics. Version 1.3. Published electronically: http://biology.fullerton.edu/deernisse/dnastacks.html

If features added since version 1.3 are used, then cite as:

Eernisse, D.J. 2003. DNA Stacks: A software package for molecular systematics. Version 1.3.3 Published electronically: http://biology.fullerton.edu/deernisse/dnastacks.html

8/24/08 (Version 1.3.5): Again, not much that is new but a few minor fixes. Webmate has been updated to improve the handling of the display of landscape vs. portrait images. Images can be zoomed (command or control with + or - key) and there are new navigation controls at the top of each image. I still use DNA Stacks regularly on my PowerBook.

2/8/06 (Version 1.3.4): Not much is new but I did fix the link to the EBI ClustalW server, because they changed their URL slightly. DNA Stacks is still stable using it in Classic mode. There might be a few other minor fixes. One new feature (Aligner, Data menu) allows for reordering taxon names that are in Aligner, for example, "AAA_BBB_CCC_DDD" can be changed to "BBB_CCC_AAA_DDD." This does not yet work for external files not already in Aligner.

7/31/03 (Version 1.3.3): Added improvements to "Extract GenBank Features" and made several minor improvements to file naming conventions. The mitochondrial genomes now supported include many new "Pancrustacean" gene orders only recently available. No attempt has been made to update the many new vertebrate genomes that have appeared, and many new insect genomes have likewise been ignored. An Excel-format spreadsheet of information pertaining to mitochondrial genomes has been added, which is an expanded version of my own system of keeping track of these genomes and the corresponding documentation.

9/5/02 (Version 1.3.2): Added a substantial new feature "Extract GenBank Features" from the new Genomics menu of any gene map card. This allows extraction of the following from any GenBank-format file but especially useful and tested for entire eukaryotic chromosomes, such as any of the chromosomes of C. elegans: 1) Excel-format features table; 2) entire sequence in string format; 3) individual exons in string format; 4) individual introns in string format; 5)individual intergenic regions in FASTA format; 6) assembled exons (cDNAs) in string format; 7) translated cDNAs in string format. This combination of new Genomics features allows many powerful investigations. The other menu options under the Genomics menu make it more convenient to do various mitochondrial gene order features that have been rather hidden in DNA Stacks for some years. These include the export of mitochondrial gene orders in formats compatible with Jeff Boore's MGA Source Guide (http://www.jgi.doe.gov/programs/comparative/MGA_Source_Guide.html) and also various recent gene order comparison software such as GRAPPA (http://www.cs.unm.edu/%7Emoret/GRAPPA/) and BPAnalysis (http://www.cs.washington.edu/homes/blanchem/software.html). It does not yet support the extended Nexus format used by the newer program GoTree (see http://www.mcb.mcgill.ca/~bryant/GoTree/). The available gene orders can also be exported as data matrices in various formats that were original to this package, including a format functionally equivalent to what has more recently been dubbed MPBE-format (but that format more efficiently encodes the data without redundancy). A variety of other small fixes are included in this release.

3/7/01: Fixed transition/transversion report script. Was previously not handling alignments with gaps properly. Only updated "DNA Translator" stack and added this file in the self-extracting archive first posted 12/00.

4/7/01 (Version 1.3.1): The following changes should improve one of the common recommended uses of DNA Stacks. This is the situation for producing an aligned selection of animal mitochondrial gene sequences from a particular gene. To accomplish this: 1) choose "Get mtDNA Sequences" from Aligner's Data menu (or use DNA Translator's gene map card's Extract menu); 2) export sequences in FASTA format; 3) align them in online ClustalW (http://www2.ebi.ac.uk/clustalw/) or ClustalX (be sure to specify "PIR" output format option and "Output Order" set to "Input" not "Aligned" before alignment in Clustal's "Output Format Options"); 4) then import the "PIR" format output back into Aligner. From here, the alignment can be checked with matching and coloring (try "Codon" or "AA Properties" for protein-coding genes), modified with the editor features of Aligner, and exported in Nexus format for phylogenetic analysis.

Fixed a bug that was introduced 6/14/00, when modifications were made to speed up "Align DNA to Current Proteins" (Data menu of Aligner Stack) for the case of long contiguous gaps. 

Also improved the "PIR" format import ("Import Options..." under Aligner's Data menu) to be more general. Before, it was only working for ">DL" (DNA linear) specifier exported by ClustalW or ClustalX, and not the ">P1" (complete protein) specifier Clustal uses for exporting protein alignments. The option now handles all possible specifier codes available for the NBRF/PIR format and, additionally, now deletes comments on the second line of each PIR-format sequence.

The "FASTA" export option (Export Options..." under Data menu of Aligner) has been further modified to account for the situation when there are '?' characters in an exported sequence. Now there is an option of replacing '?' with another character globally (automatically set to 'X' for peptides and 'N' for nucleotides). This is useful because Clustal will strip '?' characters at import. If one then attempts to use "Align DNA to Current Proteins" (see above) the peptide strings will no longer correspond to the nucleotide strings. This might be useful for nucleotides in the case where there is an internal unknown portion of the sequence that you want preserved in the Clustal alignment. Regardless of whether this option is selected, "?" (or "N" or "X") characters are now stripped from the end of each sequence. Also, any "@" and "*" characters are stripped (e.g., those added at the end of peptide sequences translated by DNA Stacks).

Fixed a problem with the display of genetic codes to choose from during coloring of nucleotide alignments in Aligner.

Features added:

Now Aligner automatically detects any selection of sequences derived from the "Get mtDNA Sequence" (see above) menu item of Aligner's Data menu when coloring is requested, as long as the three-letter starting codes for each sequence has not been changed. It might be possible that a user has a set of sequence names that all start with one of the three-letter codes used, in which case Aligner might now incorrectly assign animal mtDNA codes to the coloring. I have not yet figured out a way to avoid this without adding another option dialogue box, but one could work around this new automatic feature by starting any one of the sequences with "z" (which is never used as a first character). Because this new feature is relatively fast, I removed the automatic addition of the codes to the end of the sequence names.

Added automatic launch of two websites from the Go menu of Aligner. This depends on the LaunchURL XCMD, which in turn depends on your Mac being set up with the current "Internet Config" software (most Macs are these days). First, Aligner will now launch the DNA Stacks website, where the current version can be downloaded. Second, EBI's ClustalW Web server can now be launched. This makes it more convenient to perform a Clustal alignment as above. Remember to export a current alignment (or string sequences on disk) in FASTA format, and remember to choose "PIR" output and "Input" (not "Align") as the "Output Order." When the server has completed the alignment, long-click on the provided link and save the file to disk with a name such as "myalignment.pir" (TEXT format in Netscape). Then choose "Import Options..." from Data menu of Aligner and "PIR" as the format type. You should now have aligned sequences but, of course, you should carefully scrutinize any such automated alignment, which is where the "Match" menu item, "Color" menu items, and editing features of Aligner might help.

Added a new pull-down menu button at the upper-left corner of the Aligner window, just above the sequences. When this is pulled down, a list of the names in the sequence names field drops down, and any of these that is selected will then become the selected sequence. If the sequences came from the "Get mtDNA Sequences" (see above) menu item of Aligner's Data menu, then the pull-down menu will automatically contain the common names instead of the more cryptic three-letter abbreviation names. If they came from "Get mtDNA Seqeunces" and the user depresses the optionKey before pulling down the menu, the menu will contain the scientific binomial names. Likewise, the commandKey lists an abbreviated phylogenetic name (e.g., "Met_Deu_Ch_Hsa" for "Metazoa-Deuterostomia-Chordata-Homo sapiens), and the shiftKey lists the accession numbers. Eventually, I may also add the option of exporting one of these choices as replacement sequence names.