Overview of Help-Pages

MatInspector release notes

February 2010: MatInspector Release 8.02

Data library changes:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 8.2):
  • Includes 60 new matrices (10 vertebrate, 7 plant, 43 insect).
  • Library contains now 1166 matrices in 386 families.
• Updated Restriction Site Library (based on REBASE version 001).

July 2009: MatInspector Release 8.01

Data library changes:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 8.1):
  • Includes 132 new matrices (101 fungi (yeast), 27 vertebrate, 2 plant, 1 insect, 1 general core promoter element).
  • Library contains now 1106 matrices in 364 families.
• Updated Restriction Site Library (based on REBASE version 907).

April 2009: MatInspector Release 8.0

New features and main changes from Release 7.7.3.1:

• New lines of evidence to support MatInspector matches:
  • Known cocitation (only available on Genomatix server and GGA)
  • Known interaction (only available on Genomatix server and GGA)
  • Promoter Modules
• Improved input features to select promoters from ElDorado/Genomatix Promoter Database to MatInspector.
  • Use combo box to select gene of interest
  • Map sequence(s) to any organism available in ElDorado
• Interactive result tables that allow sorting and filtering.

December 2008: MatInspector Release 7.7.3.1

New features and main changes from Release 7.7.3:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 8.0):
  • Includes 178 new matrices (174 vertebrate, 3 plant, 1 fungi).
  • 155 of the new matrices describe homeodomain transcription factor binding sites.
  • 16 of the new vertebrate matrices are derived from ChIP-Chip or Chip-Seq experiments. These matrices describe binding sites for the following transcription factors: CMYC, CTCF, ESRRB, GKLF, HNF3B, HNF4A, NMYC, NRSF, OCT3/4, SOX2, STAT3, TCFCP2L1, USF1, ZFX.
  • Library contains now 974 matrices in 325 families.
• Updated Restriction Site Library (based on REBASE version 812).

July 2008: MatInspector Release 7.7.3

New features and main changes from Release 7.7:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 7.1):
  • Includes 31 new matrices (19 vertebrate, 5 plant, 7 core promoter elements).
  • Library contains now 799 matrices in 314 families.
  • New matrix group "General Core Promoter Elements" introduced.
  • Matrix group "Others" removed (matrices have been moved to other groups).
  • IUPAC consensus sequence of matrices include also triple-degenerate IUPAC codes (more information).
• Updated Restriction Site Library (based on REBASE version 806).

January 2008: MatInspector Release 7.7

New features and main changes from Release 7.6.2:

• New output format of the match table (e.g. matrix family descriptions are included).
• For single sequence searches, an interactive graphics with the possibility to filter matches is displayed.
• Speed-up of p-value calculations in common TF searches.

November 2007: MatInspector Release 7.6.2

New features and main changes from Release 7.4.8:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 7.0):
  • Includes 36 new matrices (26 vertebrate, 8 plant, 1 insect, 1 other element).
  • Library contains now 773 matrices in 306 families.
• Updated Restriction Site Library (based on REBASE version 711).

May 2007: MatInspector Release 7.4.8

New features and main changes from Release 7.4.4:

• The interactive SVG graphics is replaced by Genomatix Java Graphics.
  • The interactive graphics is implemented as Java applet, running within your web browser requiring a Java plug-in.
  • The Genomatix Java Graphics is faster than the SVG graphics and has more features (e.g. exporting selected regions of the graphics). For more details see the graphics overview.
• Previous versions of the matrix library can be selected in order to re-produce old results.
  • Per default the latest version (currently Matrix Library 6.3) is used.
  • Matrix Library versions to select are: Version 6.1, 6.2, and 6.3.
• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 6.3):
  • Includes 27 new matrices (21 vertebrate, 6 plant).
  • Library contains now 737 matrices in 301 families.
• Updated IUPAC library of plant transcription factor binding sites
  • Based on PLACE Release 30.0.
  • Includes 431 TF binding sites in 323 IUPAC families.
• Updated Restriction Site Library (based on REBASE version 704).

November 2006: MatInspector Release 7.4.4

New features and main changes from Release 7.4.3:

• New Project Management: (only available on the Genomatix server)
  • "Result Management" and "Sequence Management" have been combined into the new "Project Management".
  • Grouping of results and sequences into projects possible.
  • Comments can be added to projects and results.
• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 6.2).
  • Includes 8 new matrices (7 vertebrate, 1 insect).
  • Library contains now 713 matrices in 296 families.

August 2006: MatInspector Release 7.4.3

New features and main changes from Release 7.4.1:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 6.1).
  • Includes 41 new matrices (33 vertebrate, 5 plant, 3 insect).
  • Library contains now 705 matrices in 294 families.
• Updated IUPAC library of plant transcription factor binding sites
  • based on PLACE Release 27.0
  • includes 419 TF binding sites in 315 IUPAC families
• Updated Restriction Site Library (based on REBASE version 607).
• Color code for matrix similarity column introduced:
  A green background in the matrix similarity column marks a similarity above optimized, a red background marks a similarity below optimized (e.g. if a search was started using "optimized - 0.02)".

December 2005: MatInspector Release 7.4.1

New features and main changes from Release 7.4:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 6.0).
  • Redefinition of all matrices originally based on the TRANSFAC matrix library. This way we achieved more specific matrices because of a better alignment of the binding sites and/or removal of weak binding sites. Furthermore, some erroneous matrices could be corrected.
  • Includes 56 new matrices (35 vertebrate, 12 plant, 2 insect, 7 fungi).
  • Library contains now 664 matrices in 284 families.
• Updated IUPAC library of plant transcription factor binding sites
  • based on PLACE Release 21.0
  • includes 399 TF binding sites in 298 IUPAC families
• Updated Restriction Site Library (based on REBASE version 510).
• Sequence Management: Upload of new sequence files to the user's personal sequence directory possible.
• Download of results as PDF file possible.

March 2005: MatInspector Release 7.4

New features and main changes from Release 7.3:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 5.0).
  • Includes 42 new matrices (35 vertebrate, 6 plant, 1 other matrices).
  • Library contains now 634 matrices in 279 families.
  • Additional feature for vertebrate, plant, and insect matrices: percentage of promoter sequences from ElDorado in which a match to the matrix / matrix family is found with optimized matrix similarity.
• Updated IUPAC library of plant transcription factor binding sites
  • based on PLACE Release 18.0
  • includes 384 TF binding sites in 287 IUPAC families
• Updated Restriction Site Library (based on REBASE version 502).
• Search for common TF sites:
  • A significance value (p-value) is computed for each common TF site.
  • Summary of common TF sites is displayed as table in addition to the (now optional) graphics output.
  • Excel export of summary of common TF sites possible.
• When MatInspector is started only the most important parameters are shown. All other parameters can be changed when the "More options" icon is pressed.

September 2004: MatInspector Release 7.3

New features and main changes from Release 7.2:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 4.2).
  • Includes 28 new matrices (18 vertebrate, 9 plant, 1 mitochondrial matrices).
  • Library contains now 592 matrices in 267 families.
  • Plant transcription factors are assigned to the plant matrix families (389 transcription factors from several plant species).
• Revised IUPAC library of plant transcription factor binding sites
  • based on PLACE Release 16.0
  • includes 377 TF binding sites in 285 IUPAC families
• Updated Restriction Site Library
  • Based on REBASE version 408.
  • Identical restriction sites are merged to one family.
• Search for common TF sites: the lower limit of sequences which has to contain the common sites can be defined by the user.

March 2004: MatInspector Release 7.2

New features and main changes from Release 7.0:

• Extended weight matrix library of transcription factor binding sites (Matrix Family Library Version 4.1)
  • Includes 29 new matrices (10 plant, 17 vertebrate, 1 insect, 1 nematode matrices).
  • Library contains now 564 matrices in 262 families.
• Extra output added: matches can be displayed aligned with the sequence.
• Nucleotide distribution matrix is shown on matrix help page.
• Matches that occur at the same position on the (+) and (-) strand are no longer merged. They are shown both in the output to facilitate the identification of strand-specific common sites.
• Export of matches to Excel format possible.

December 2003: MatInspector Release 7.0

New features and main changes from Release 6.2:

• Extended weight matrix library of transcription factor binding sites (Matrix Family Library Version 4.0)
  • Includes 50 new matrices (34 plant, 13 vertebrate, 2 insect, 1 fungi matrices).
  • Tissue information added for vertebrate matrices.
  • Library contains now 535 matrices in 253 families.
• Revised IUPAC library of plant transcription factor binding sites
  • based on PLACE Release 14.0
  • includes 363 TF binding sites in 278 IUPAC families
• Matrices used for the analysis can be filtered by the tissues they are associated with.
• Matrix family help page lists the transcription factors that are represented by the family.
• Export of matches to GenBank format (feature table) possible.
• Faster access to sequences entered as database accession numbers.

June 2003: MatInspector Release 6.2

New features and main changes from Release 6.1:

• Revised weight matrix library of transcription factor binding sites (Matrix Family Library Version 3.1)
• Matrix thresholds like "optimized+0.05" are allowed

January 2003: MatInspector Release 6.1

New features and main changes from Release 6.0:

• Additional graphics showing common transcription factor binding sites
  • Available in the PNG format or as interactive SVG document
  • SVG version provided with filter functionality

December 2002: MatInspector Release 6.0

New features and main changes from Release 5.3:

• Revised weight matrix library of transcription factor binding sites (Matrix Family Library Version 3.0)
  • Contains 41 new weight matrices (1 bacteria, 40 vertebrate matrices).
  • All matrices of a matrix family are now of the same length. This results in identical positions for the individual matrix matches of a family.
  • The library contains now 452 matrices in 216 matrix families.
• You can search if the transcription factor binding sites you are interested in are represented by our matrix library.
• New IUPAC library containing plant transcription factor binding sites:
  • based on PLACE Release 11.0
  • includes 323 TF binding sites in 258 IUPAC families

August 2002: MatInspector Release 5.3

New features and main changes from Release 5.2:

• Graphical representation of the search results
  • Browsers provided with an SVG plugin (available at the Adobe web site) will display an interactive SVG graphic. (More on SVG can be found at W3C's SVG pages.)
  • Otherwise a graphic in the PNG format is shown. (The SVG plugin is not available for all systems.)

May 2002: MatInspector Release 5.2

New features and main changes from Release 5.1:

• Revised weight matrix library of transcription factor binding sites (Matrix Family Library Version 2.4)
  • Contains 32 new weight matrices (1 bacteria, 8 plant, 23 vertebrate matrices).
  • Matrix families that do not describe transcription factor binding sites were moved to a new group called "Other functional elements".
  • The library contains now 412 matrices in 193 matrix families.
• Secondary accession numbers (including secondary accession numbers pointing to several sequences) are accepted as input.
• Sequences of matrix matches can be extracted.
• Vertebrate section is now default for matrix group selection
• Scanning of complete database sections is not possible anymore as is has shown to confuse users.

September 2001: MatInspector Release 5.1

New features and main changes from Release 4.3:

• Revised weight matrix library of transcription factor binding sites (Matrix Family Library Version 2.2)
  • Contains 20 new weight matrices (2 fungi, 7 insect, 1 plant, 10 vertebrate matrices)
  • Revised matrix family classification
  • All matrix descriptions are revised, references are available for each matrix
  • Consistent nomenclature of matrix identifiers
• MatInspector now accepts input sequences in plain format.
• For long jobs, users can enter an email where the results are send after the job is finished.
• Enhanced output: added color code for highly conserved base pairs in matrix match
• Available databases (on Genomatix Server)
  • NCBI Reference Sequences (mRNA sequences) are available as additional database
  • EPD and mRNA RefSeq accession numbers (starting with NM_) can be entered in addition to EMBL/GenBank accession numbers