The University of Arizona
TCW Release Notes
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TCW Version 2.1 (6 Nov 17)
First release 25 Oct 17, update 11/6/17: fixed problem where it was not working with JDK v9.

viewSingleTCW:

  1. N-fold: The N-fold filter has been re-written to have the same look as the N-fold column, and be easier to use. Also, a bug was fixed where if the divisor was zero, the N-fold pair was not shown in the table. The N-fold column now sorts like the DE columns by absolute value.
  2. Decimal numbers:The ability to change how decimal numbers were displayed has been moved from the Sequence Table Column panel to its own panel, which is shown in the upper left. This change was made because the formating is used for all tables. Additionally, the formating options have changed to give more flexibity and be simipler to use.
  3. The percentage of sequences in table is now displayed at the top of the table.

TCW Version 2.0 (23 July 17)
This version was previously released on 10July17; this update improved the codon alignment algorithm and alignment display in viewMultiTCW.

This is a major release for the multiTCW, though there are also a few significant changes for singleTCW.

runMultiTCW

  1. The interface is much cleaner -- too many changes to list.
  2. Add Pairs is a separate step, which adds all pairs that have a blast hit, which can be queried in viewMultiTCW
  3. Add statistics to pairs is a separate step. This is relevant when the singleTCWs were created from transcripts (i.e. DNA). The statistics include:
    • Synonymous, nonsynonymous, and degenerate codons.
    • Transitions and tranversions.
    • CpG sites and GC content.
    • Ka/Ks values, where are obtained from KaKs_calculator (Zhang et al. 2006). The pairs file is written to disk, the user runs KaKs_calculator on the file, then had runMultiTCW read in the results.
  4. The GO (gene ontology) are imported into the database on creation.
  5. The Transitive clustering routine has been replaced with Closure clustering, which guarentees that all sequences in a cluster have a blast hit with all other sequences in the cluster, and that each sequence has a user supplied overlap and similarity score with at least one sequence in the cluster.
  6. Some improvements to the BBH clustering routine.
  7. Two new example projects are included that have good homology. They are referred to in the mTCW UserGuide.
viewMultiTCW
  1. Pairs:
    • Add new Pairs Table.
    • Add filters on blast scores, and all statistics stated above..
    • Provides alignment of both AA, NT, CDS for pairs.
  2. Cluster:
    • Add link to pairs and sequences tables, i.e. all pairs in the cluster are shown in the pairs table, and all sequences in the cluster are shown in the sequence table.
    • The RPKM and DE filters have been removed, as they were pretty meaningless. The new links to the sequences allow easy viewing of these details.
  3. Sequences - added filters:
    • Cluster methods
    • RPKM values
    • Sequences with Blast hits to different set (i.e. not from same singleTCW)
    • Has Annotation or has GO.
  4. Export on all three tables now includes exporting GOs and sequences.
  5. All three tables have 'Copy' button to copy various information to clipboard.
runSingleTCW:
The ORF finder has been updated. To use it on an existing sTCW database, just run ./execAnno <project_name> -r.
  • The ORF finder use to use the longest ORF that agrees with the hit frame, where the ORFs were basically the same as found with the NCBI ORF_finder. When working with the BBH in multiTCW, it became clear that for de novo transcripts, when there is a hit to the sequence, it is better to use the hit ends -- which is what it does not.
  • ORFs no longer will contain strings of n's.
  • The names of the ORF files have been changed in the ORF directory, and it writes the file of proteins (translated best hit) to th projcmp/AAfiles directory for easy use in runMultiTCW.
  • More elaborate GC statistics are computed to be shown in the overview.
viewSingleTCW:
  • Overview: Change annoDB <40% to Eval>=50 and Total>=50 Includes the average length of UTRs and CDS, and GC and CpG for UTRs and CDS
  • Basic GO query: Added Show 'Sequence - best hit with GO'. This helps to understand how the best-evalue was assigned
  • Basic Hit query: Added column of all GOs and column of #GOs for hit. Added 'Show all assigned and inherited GOs for hit'
  • Export on Main Sequence table:
    1. Allow appending to existing file.
    2. GO: add term_type filter. Add option for 'per sequence' and 'overall', where the first applies the evalue to each GO-seq bestEval and the second applies the evalue to the overall GO bestEval
    3. Remove writing PCC files.
    4. Check for write access (may not have it from Applet).
Bug fixes in singleTCW:
  • Even when downloading the GO mysql on the same day as UniProt, I have had them be out of sync, which caused an error in runSingleTCW; this has been fixed.
  • Overview of viewSingleTCW: the coverage was wrong.
  • Basic GO Query: if #Seqs selected, E-value filter was ignored.
  • Pair alignment: gaps were not shown in graphic view (bug just in last release)

TCW Version 1.6.8 (03 Jan 17)

  1. runMultiTCW
    1. The user interface is much easier to use, and better error messages.
    2. The user can now have mTCW run a self-blast on the protein or DNA sequences to be used for clustering.
    3. The BBH (Bi-directional best hit) has now been added as a clustering method. It only works well if there are only two datasets being compared since it only allows clusters of size two, i.e. they are the reciprocal best hit over all hits.
    4. BBH and Transitive can use the protein or DNA blast files for clustering.
  2. viewMultiTCW
    1. The user can view the protein or DNA alignment. They can also click on an alignment to see the text form in the canonical multi-row format.
  3. viewSingleTCW
    1. Basic Hits: (1) Added a 'Show' button so show all columns for the selected row. (2) Added seqStart, hitStart, seqLen, and hitLen columns. (3) Add a copy to clopboard for the descripton or sequence of the selected hit. (4) Fixed a bug where the nucleotide alignment did not work if one sequence was upper case and the other lower case.
    2. Export: The tables now have column headings writen as first row, and the output from the different interfaces is more systematic.

TCW Version 1.6.7 (29 Nov 16)

  1. Sequence Pairs:
    1. TCW has an option to compare sequences in the database; this has been improved.
    2. The interface has more options for viewing Pairs.
  2. Basic GO:
    1. The DEtrim features has been added back.
    2. An 'Add to table' has been added.
    3. The ability to delete rows has been added.
    4. Basic GO has new options that act on the entries in the GO table:
      1. Show All ancestors - shows the ancestors for the the entries in the GO table.
      2. Show Longest Paths - determines all paths for all the entries in the GO table, then removes ones that are contained in a longer one.
      3. Export All Ancestors, Export Longest Paths, Export All Paths - writes the respective information to file.
  3. An 'Add to table' has been added to the Basic Seq and Basic Hit panels.
  4. An 'Align' option has been added to the Basic Hit panel; this can show the alignment of multiple sequences to a hit.
  5. Overview: Fixed a little bug on the percentages of GO DE terms.

TCW Version 1.6.6 (28 Oct 16)

  1. runSingleTCW: some additional changes were necessary to accommodate the changes to nr.gz, as a few things in viewSingleTCW did not work. To get the fixes, reload the annotations; i.e. ./execAnno <project> -q (this deletes the existing annotations, and reloads from the existing blast .tab files). Also, some slight changes were made to the rules for selecting the best annotation hit.
  2. viewSingleTCW:
    • Basic Hit Query: a filter on percent similarity was added, along with the column for it and aligment length.
    • For both Basic Hit and Basic GO, the query form was made more intuitive.
    • Sequence Details: a column was added to the Hit table to indicate the TCW selected Best E-val, Best Anno, and Best GO.

TCW Version 1.6.5 (10 Oct 16)
This release adds evidence codes (EC) to the single TCW database; it is necessary to run "Exec GO Only" from runSingleTCW to get the codes; no error occur in viewSingleTCW if the EC have not been added.

  1. runDE:
    • The p-values can be read from a file versus being computed.
    • The overview can be updated from the runDE interface.
    • An 'Exit' button has been added which will also exit R.
    • A tiny bug has been fixed for the "GOseq" execution -- except for an unusal situation, it will only have minor effect on the p-values.
  2. runSingleTCW:
    • The evidence codes (EC) have been added.
    • The format for NCBI nr database changes; TCW has been updated so that it will read the new or old format.
  3. viewSingleTCW - Basic GO Query:
    • The evidence codes can be queried from the "Basic GO" interface.
    • An additional filter has been added on the number of Sequences (gene products) associated with each GO.
    • The maximum number of GO levels was 16; its now dynamic and may go above or below this number.
    • Multiple GOs can be selected in order to view the sequences associated with all selected GOs.
    • The DE trimmed feature is currently disabled, as recent changes have broken the algorithm.

TCW Version 1.6.4 (21Sept16)

  1. viewSingleTCW:
    • Status output has been added to the Blast page.
    • Basic Hit Query, the annoDB option: it was the case that only one or all annoDBs could be selected; now, any subset can be selected.
    • Basic GO Query: query on GO Slims has been added.
    • Sequence Details: an option has been added to view all assigned and inherited GOs.
  2. runSingleTCW:
    • GO slims can be added from the GO database or from a user supplied OBO file.
    • When building the database, indicies have been added for the Hits so that queries for the Basic Hit tend to run faster.
    • For annotation: If the tabular search file is supplied, the corresponding FASTA file may be zipped (as before, it can also be zipped for diamond, but not for blast).

TCW Version 1.6.3
The release is on changes to viewSingleTCW.

(4Sept16)

  1. Fixed two bugs: (1) viewSingleTCW would not startup right if there was only one library. (2) Could not view a RPKM or DE column in Basic Hits if there was no GO annotation.
  2. GO Annotation: (1) Basic GO Annotation: There are more ways to look at ancestor and descendants. (2) Sequence Detail: The hits with inherited GOs can now be viewed. (3) Rearrangment of the GO query panel to make it more logical.

(16Aug16)
  1. Basic Hit Query: filters have been added for RPKM and DE p-values, i.e. the hits that pass the filters must have at least one sequence that passes the RPKM and/or p-value filter.
  2. All queries result in a description of the filter used, which is placed over the table.
  3. Basic Sequence: this has been simplified.

TCW Version 1.6.2 (8Aug16)
The release is on changes to viewSingleTCW.

  1. The tabs for Sequence Panels are positioned under their respective list instead of all under "Show All".
  2. Basic Hit Queries: The Limit entry box is removed, and the 'Best Eval' and 'Best Anno' checkboxes are moved from Attributes to the front panel. A new columns is added called '#Best' to indicate whether the hit is a assigned the best hit for any sequence that aligned to the hit; this will always be >0 if 'Best Eval' or 'Best Anno' is selected.
  3. All searches are queued so that TCW is not frozen during database retrieval.

TCW Version 1.6.1 (16July16)
The release is on changes to viewSingleTCW.

  1. All writing to disks has been removed except for writing to Java Preferences, where TCW will not fail if the user does not have write permission.
  2. The columns panel for Sequences has been condensed.
  3. Some features were removed that were mainly useless.

TCW Version 1.5
Release dates from 24 March 2016 to 7 June 2016
The major changes are: (1) runAS provides a graphical interface for the annotation setup. (2) New demo files. (3) More options for querying GO in viewSingleTCW.

viewSingleTCW

  1. The Sequence Results table provides a description of the filters applied for the corresponding table.
  2. The Export on the Main Sequence Table did not always work on some machines, that has been fixed.
  3. Basic Sequence and Basic Hit Query have been greatly modified for clarity. The Species selection for the Basic Hit Query has been improved.
  4. An option to view the GO paths for a selected GO has been added.
  5. The GO List and GO Tree outputs are clearer, and the GO Help has been added to.
  6. Added an option to export the replicates for all seqIDs in the sequence table.

runAS

  1. A Java interface has been created for the "Annotation Setup". It guides the user in downloading the UniProt taxonomic database and building the GO database. It replaces the original Perl scripts, and is faster and uses less memory. See Annotation Setup (12 April 2016).
  2. runAS (Annotation SetUp) has been updated to provide better messages and use less memory (29 April 2016).

runSingleTCW has been updated to provide much better error messages and some small bugs were fixed.

New demo files with recent annotations. The old ones work fine, but the annotations are 4 years out of date and the sequence quality is not as good. Plus, the new demos include (1) a protein sequence demo, and (2) quality values for the mixed Illumina transcripts and Sanger assembly.

Release 14 March 2016 -- New GO Features in viewSingleTCW
To use the new features on pre-March 14th built TCW databases, it is necessary to
(1) update the TCW GO tables (./execAnno <database name > -G) and then (2) rerun the runDE GOseq option.

  1. Basic GO annotations display: has multiple new options to show information about a selected GO, i.e. showing the ancestors as a list, ancestors as a tree, and descendants. It also has a few more count columns in the table to distinquish hits that have been directly assigned to a GO in the UniProt files versus hits that are descendants of a GO, hence, are inherited.
  2. Basic AnnoDBs display: has an option to show the GOs assigned to a selected hit.
  3. View Sequence: has options to show hits, ancestors or tree associated with a selected GO.
  4. A new best hits column: the Best Eval and Best Anno do not always have GO annotations. The new "Best Hit With GO" is the best e-value with GO annotations.
    • Select on "Columns".
    • Filter under "Best Hit".
    • Displayed in Sequence details.
  5. Sequence details shows differential expressions values.
Additionally, the GO tables in the TCW are significantly smaller (30%).

TCW Version 1.4

Release (1 Mar 2016)
This release has changes for exploring the details of a selected sequence from the sequence table.

  1. The options for the sequence detail page are restructured for clarity (Detail, Frame, Go, Hit Alignment).
  2. For hit alignment, a new display is available to show the alignment in a format like UniProt uses, i.e. multi-line where a "+" is used for synonymous match, the amino acid is shown for exact match....
The version works on previously built v1.4 TCW databases.

Release (8 Feb 2016)
To use the new features on previously built TCW databases, it is necessary to
(1) reinstall the GO database (i.e. newGOver.pl), (2) update the TCW GO tables (./execAnno <database name > -G) and then (3) rerun the runDE GOseq option.

  1. Add GO and Interpro:
    1. Basic Query Sequence - add best GO and Interpro as columns
    2. Basic Query annoDB - add GO and Interpro as columns and filters fot these to the Attributes
    3. Main Table Column - add as columns for Best Eval and Best Annotation
  2. Basic Query GO
    1. A filter has been added for e-value, where the e-value assigned is the best of all UniProt-Sequence hits that contain this GO.
    2. For a selected GO, the following options are available:
      • Show....
        	all hits mapped to the GO (assigned only)
        	all hits mapped to the GO (assigned or child)
        
        This display shows the evidence code for assigned hits.
      • Copy GO Term to clipboard
      These options are explained in detail on the Basic Query GO Help page.
  3. Sequence Details -- View GOs (optional selected):
    1. If no selected hit, show union of assigned hits with evidence codes
      A "Hits for selected" button allows the user to see all the {HitID, e-value, EC, %sim) for the GO.
    2. If selected hit, show assigned and ancestor GOs, and all assigned Interpro, enzyme EC, KEGG, and Pfam identifiers.
  4. Overview contains GO version and a table of GO p-values.
  5. Changed Basic annoDB Hit:
    1. Add 'Load File' so a list of hit identifiers or descriptions can be loaded together (the Load File is also on the Basic Query Sequence page).
    2. When a search string is entered, check "Use Filters" if the filters should be used in addition to the search string.
    3. Default in Attributes changed from Best Eval to Best Anno
  6. Bug fix:
    1. Blast feature: if there were n's in a nucleotide sequence, and was assumed to be protein.
    2. Columns KEGG, EC and PFam: if one of these was selected for both Best Eval and Best Anno the same identifier was shown in both columns.
Changes to UniProt/GO installation scripts:
  1. newGOver.pl - add GO version to the local go database and add GO and InterPro to TCW UniProt table to the local go database used to build TCW GO tables.This script needs to be rerun, and the TCW go tables updated (./execAnno -G)
  2. newUPfull.pl - The full .dat is not downloaded with the newUPver.pl since it is so big and only a subset of it is typically used. However, that means there will be no GOs for the subset; this script downloaded the .dat files. It should be run after newUPver.pl and before the newGOver.pl is run.
Next release: there will be another release with more GO improvements within a month. Three improvements will be:
  1. the MySQl hit-GO tables can be very big as it contains both assigned and ancestor relations; this will be reduced to just assigned.
  2. an improved view for the GO tree
  3. a filter will be included for the evidence code.

TCW Version 1.3

Version 1.3.9 (10 Dec 2015)

  1. runDE:
    • Upgraded DESeq to DESeq2. EdgeR works with their latest release (Oct 2015).
    • For the built-in EdgeR and DESeq2, their p-value adjusted values are used, so the checking TCW FDR is not necessary.
    • EDASeq has been removed as it can be executed with an R-script if desired.
  2. Terminology has been updated to reflect current practices.

Version 1.3.8 (30 Nov 2015 - 5 Dec 2015)

  • This release had a major feature added to the runDE program, which computes differential expression using published DE methods that execute in the R environment. The changes are as follows:
    1. It was the case that there were three methods available, however, they can get out-of-date and new methods published, and there was no way for the user to change them without changing the TCW code. In this release, there is a new option to supply an R-script. The needed values (e.g. matrix of counts) are written to the R environment, the R-script is run using the supplied variables, and the results are read and entered into the TCW database. runDE has an option to filter sequences that have low read counts before computing DE.
    2. The interface has been restructured for clarity.
    3. Can now run "runDE <database>", which by-passes the sTCW database chooser.
  • This version works with Diamond release 4/2015.
  • Some oddities in the runSingleTCW were cleaned up.

Releases 2 Oct 2015 - 8 Nov 2015)
This release contains further enhancements to the ORF finding algorithm. It computes codon and hexamer usage from the regions of sequence that have good annotation hits, and uses their log-likelihood ratio to select between two similar length candidate ORFs (when there is no annotation hit). It has a new display in viewSingleTCW to show the codons of a sequence in any of the 6 frames. More information can be found in TCW ORF finder.

  1. viewSingleTCW:
    1. For location, the group could be 'scaffold', 'chr', etc; these are generally followed by a number. A column was added that contains the number only, which allows numeric sorting.
    2. Added a Filter for sequences that have a location.
    3. Speeded up some operations in the Basic searches.
    4. A column has been added to viewSingleTCW that is the count of the n's within a sequences.
    5. The n's can be viewed with the "Show Sequence by Frame" (upper left pull-down from the sequence detail page.
  2. runSingleTCW:
    1. For 'Add Remark', where remarks can also be removed, added the ability to remove all remarks except TCW added remarks.
    2. The options for the ORF finder are incorporated into runSingleTCW. The ORF finder options are shown on the viewSingleTCW 'Overview' at the bottom.
    3. Slight redesign to the runSingleTCW interface and the annoDB Options menu for clarity.
    4. Input fasta files may now have comment lines starting with '#'.

Version 1.3.5 (5 Sept 2015)

This release has improvements for determining the best reading frame, where the frame with a protein hit is given precedence.

Version 1.3.4 (7 Aug 2015)

  1. The code has been restructured to be clearer. The only impact this may have on users it that the applets should now reference:
    1. stcw.jar: CODE="jpave.query_interface.JPaveApplet" => CODE="jpave.viewer.STCWApplet"
    2. mtcw.jar: CODE="cmp.main.CPaveApplet" => CODE="cmp.viewer.MTCWApplet"
    And there are three jars instead of two: stcw.jar (viewSingleTCW), runstcw.jar (runSingleTCW) and mstcw.jar (viewMultiTCW and runMultiTCW).
  2. The computation of the Best Eval is now strictly the best e-value (it did have some logic to get best annotation with slightly less-good e-value). The term 'unk' has been added to the terms ignored for 'Best Annotation', as its the default description when none is provided.
  3. viewMultiTCW counted the percentage of RPKM >=1000, but was not including those with no RPKM in the total count.
  4. viewSingleTCW: the rarely used "Filter Pairs" had quit working.

Version 1.3.3 (7 July 2015)

  1. Locations: From runSingleTCW, locations can be entered using the "Add Remarks and Locations" button. The input file contains rows of (seqid, location) pairs, where the location information in the format ">scaffold:start-end(strand)", e.g. ">LG_1:100-500(-)". Note, the last version allowed the location to be the seqid from the sequence file; this allows the locations to be added after the database has been created.
  2. Minor bug fixes and changes:
    1. The viewSingleTCW overview now additionally reports RPKM ranges.
    2. The viewSingleTCW Blast option did not work for protein databases. Also, the display of the 'long' form of output had a messed-up indentation. Both have been fixed.
    3. In the calculation of the 'Best Annotation': any hit with description "unknown" is now omitted (this is used by Genbank nr). Some other minor changed were added to adapt to changes in UniProt.
    4. The annoDB hits are ranked according to their e-value -- which had been broken and is now fixed. Also, the "View Sequence" options of seeing "Best annoDB, eval & anno" was split into "Best eval & anno" and "Best annodB".
    5. In the Basic searches, using "_" in a substring was ignored by MySQL because it is a special character in MySQL (ignores any single character). This has been fixed.
    6. runMultiTCW has more checks on the input.

Release (16 Jun 2015)

Location information. This release add the ability to load location information, which is useful when the input is predicted genes (with introns removed).

  1. The input sequence fasta files can have location information in the format
    ">scaffold:start-end(strand)", e.g. ">LG_1:100-500(-)".
  2. The location information will be enter into four new columns that will be displayed in the sequence table.

Version v1.3.2 (24 May 2015)

  1. Usearch/ublast can be used for searches; it works best for protein to protein.
  2. The search program can be selected on the runSingleTCW interface; e.g. to run blast on SwissProt where we want hits in the gray zone, but run diamond on Trembl for speed but do not get the hits in the gray zone.
  3. Existing annotation can be removed from the runSingleTCW window.
  4. TCW works for transcripts or protein sequences, but the terminology was basically for transcripts; rewording now uses the terminology "sequences" as much as possible.
  5. viewSingleTCW has some small interface changes for clarity.

Release (3 May 2015)

  1. TCW can extract annotation from a gzipped fasta file. Note: Diamond can search against a gzipped file but Blast cannot.
  2. newUPver.pl: added option to download the full SwissProt but not the full Trembl.
  3. newGOver.pl: added error messages and detection if the GO URL no longer exists.
  4. runSingleTCW:
    • added column for fasta file (there was only a column for the annoDB),
    • fixed a problem on MACs where it did not always detect when an annoDB had already been loaded,
    • fixed a bug where the "Used Protein" query did not work right; the annotation needs to be redone for this to work on existing TCW databases (you can just reload all blast files if they still exist).
  5. viewSingleTCW: The header information on showing sequence to protein alignments is more informative.

Version 1.3.1 (27 Feb 2015)

  1. TCW provides the option to use Diamond for searching protein databases. Diamond executes blastp and blastx-like searchers, producing the same output with very similar e-values. It is awesomely fast!! Though note, it misses some low similarity hits that Blast gets. See using diamond for details on using this program in TCW and performance.
  2. TCW use to read an old NCBI refseq format, but it is not compatiable with NCBI nr format, so TCW has been upgraded to read NCBI nr format. NOTE: GO annotation is only provided for UniProt hits as it reads the necessary information from the UniProt .dat files.
  3. A few small schema (i.e. database) additions for the following:
    1. A new column to provide the number of NCBI hits for a sequence/contig (it already has #Swiss, #Trembl, #NT in viewSingleTCW, Select Columns).
    2. The viewSingleTCW Overview is updated to show better statistics for the annoDB hits.
    If you have an existing TCW databases, view it with viewSingleTCW and it will be automatically updated.
  4. ./execAnno <project name> -a removes the current annotation only. This is useful if you want to try different parameters. That is, if the database contains the hits for an annoDB, runSingleTCW will not let you edit parameters to re-run diamond or blast; this will remove the annotation so you try different parameters easily.
  5. The execAnno/runSingleTCW provides clearer trace output, and multiple other little changes for clarity. A few tiny bug fixes.

Release (28 Dec 2014)

On viewSingleTCW, in the "Select Columns and "Filter Query" panels, it now shows the library Title next to the column name and the library names that were used in a DE calculation. For the Library Title, if it does not have one, you can add it with the runSingleTCW. For the library names to show for the DE column, you need to rerun the DE calculations using runDE.

Release (27 Nov 2014)

  1. The signed applet displayed SyMAP instead of TCW
  2. All the exec scripts (e.g. execAnno) had the wrong path to the jar file

Release (28 Aug 2014)

There are no major changes of functionality for this release, however there are some substantial alterations.

  1. The applets have been signed with a proper certificate to minimize security popups and blocks.
  2. Multi-host browsing capability has been removed as being too prone to problems. Now, HOSTS.cfg can only contain one host/username/password set, and this will be used for all operations.
  3. Mac OSX binaries have been supplied for all auxiliary programs, so all functions should now work on (64-bit) OSX without additional install.
  4. Jar files have been renamed stcw.jar and mtcw.jar
  5. For the DE feature, the path to library libjri.so has been properly included to remove the need to copy this library to a system location
  6. For connecting to the database, TCW will try several variations of 'localhost', including IP address and domain name, to reduce the need to add additional MySQL user entries
Known bugs:
  1. If you pairs computed, sometimes the pairs table shows when you select "Show all sequences"; just go to the "Filter Query" and select search and you will get the all sequence table.
  2. Occasionally when I add an annoDB to an existing project, it does not show up in the interface but it does exist internally, i.e. if you "Annotate", it is included in the annotation.

TCW Version 1.2

Release: 18 December 2013

Major changes

  1. DE values
    1. The DE values only provided signficance but not direction, e.g. if Lib1 compared to Lib2 have a low p-value, is Lib1>Lib2 or is Lib1<Lib2. Hence, if Lib1 is less than Lib2, the p-value will now be negative.
    2. You can just rerun runDE on your project(s) to update the p-values; you must also rerun GOseq. The Overview will be regenerated once you view the project again.
    3. The sort on the DE column ignores the sign so that the most signficant values will sort to the top or the bottom.
    4. viewSingleTCW: the DE Pvalues query allows you to select for each individual library pair up, down or either.
    5. viewMultiTCW: has a new query that allows you to view clusters that have similar DE values; i.e. view the clusters that have {at least one, all} members from N species that have a significant {up, down} DE values for one or more selected pairs.
  2. runSingleTCW:
    1. The Add Remarks is more robust and now allows appending remarks.
  3. viewSingleTCW:
    1. A Blast option allows the user to blast a sequence against those in the database; for applets, the user must have blast on their machine.
    2. An Export type has been added to include the level N GOs on output for the displayed sequences, where N (or a range) will be a parameter on the Export menu.

Smaller changes and bug fixes

  1. viewSingleTCW: If a single sequence or DB hit is selected in the Basic search, the "View Selected Sequence" will display it in the table instead of going directly to the Sequence Detail page, as the DE values are only available from the table.
  2. Fix bug which caused occasional truncation of annotation loading

TCW Version 1.1

Release: 16 July 2013

Major changes

  1. runSingleTCW:
    1. When defining the count files for "Generate File", a directory can be specified and all valid files automatically entered.
    2. Selecting the 'Best Anno' has been further improved when using UniProt, as whether it is a SwissProt (versus TrEMBL) is taken into account.
  2. runDE:
    1. Two ways have been added to add multiple DE columns: (1) All Pairs for Group 1, where every library selected in group 1 will be compared with all others. (2) Get Pairs from File, where the rows in the file list Group 1, Group 2 and the column name.
  3. viewSingleTCW:
    1. A trimmed set of "most interesting" GOs is computed based on GOseq p-values, if GOseq was run.
    2. The BasicGO search output has a tree view mode to see the GO hierarchy.
    3. Contig overview: the lowest level GOs are shown on the main overview page. Using a pull-down, the tree of GOs for the contig can be displayed, or a hit can be selected and only the GOs for that hit are displayed.
  4. runMultiTCW:
    1. The Pearson Correlation Coeffient may be run on all pairs of a cluster.
    2. Improved algorithm for assigning the best description to each cluster.
  5. viewMultiTCW:
    1. The percentage of PCC>=0.8 is shown for each cluster.
    2. The percentage of RPKM>1000 is shown for each cluster.

Smaller changes

  1. runSingleTCW:
    1. Bug fix: DE values could not be added with runDE to assembled contigs, which has been fixed in the assembler.
    2. Though incremental annotation was/is supported, it was cleaned up to ensure that no extract steps were performed.
  2. viewSingleTCW:
    1. Replicas can be viewed from the Sequence detail page.
    2. The display for floating points can be changed on "Select Columns", which applies to all tables that contain any floating point.
    3. On Basic DB hit page, for read libraries, the count was being shown; this has been changed to RPKM.
    4. Multiple projects can be viewed from the same viewSingleTCW startup window without problems.
    5. The #5' and #3' were wrong in contig overview. Removed columns #loners (for assembled contigs) and #Shared hits (for pairs), as these columns no longer have values.
    6. Bug fix: GO query produced an error if GO ID was selected but the go id string did not have numbers.
    7. Bug fix: error viewing sequences for GO
    8. Bug fix: proteins could not be aligned if the project was created with peptides sequences.
  3. viewMultiTCW applet:
    1. The MUSCLE button does not show on the applet, as it will not run from the applet.
    2. The Filter query view looked odd due to missing +/- icons, which has been fixed.

TCW Version 1.0

Release: 15 April 2013

There are major changes from PAVE to TCW, where the biggest are:

  1. New runDE: computes differential expression using published methods for R.
  2. New runMultiTCW: builds a comparison database from multipe single TCW databases.
  3. New viewMultiTCW: view the comparison database.
  4. The manager and viewer for a single species database (as processed by PAVE), are now called runSingleTCW and viewSingleTCW and the database is referred to as the sTCW database.
    1. When using UniProt for annotation, the GO, Pfam, EC and KEGG identifiers are extracted and added to the sTCW database. The GO database is used to add the GO level information. The viewSingleTCW has a "Basic GO Query".
    2. The runSingleTCW will take protein sequences and quantitative counts as input (hence, the sequences in TCW may be assembled consensus sequences, gene models or proteins, so the generic term 'sequence' is used for all these cases). All the other TCW programs can also use protein sequences.

There are also many small feature enhancements and some bug fixes. Here are some of them:

  1. The "1st best hit" has been changed to the "Best Eval" and the "Best Hit" has been changed to the "Best Anno", where the second uses the hit that does not have phrases such as "uncharacterized protein" in its description.
  2. Either the new Blast+ or the legacy Blast can be used.
  3. Remove all usages of InnoDB.
  4. A new column of fold change has been added to viewSingleTCW.
  5. Tables can be 'copied' to the clipboard.

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Email Comments To: tcw@agcol.arizona.edu