What is SeqPad?

SeqPad combines advanced sequence data gathering and data visualization with an intuitive integrated user interface.

Underneath, SeqPad extensively uses some high-quality and well-known open-source framworks like biojava, hibernate, piccolo2D, jakarta commons and several, several others!

Download, now ...

for the not-so-patient readers, we have prepared an all-inclusive download package based on the latest stable release.
tips for building and running seqpad are included !

http://www.seqpad.org/snaps/

Feature List (short version)

[ 1. Data gathering & import]

• SeqPad integrates with the major public bioinformatics tools for sequence similarity searching via plug-in and/or web service technology

e.g. NCBI Blast, BDGP, BDGPSplice, ClustalW, CODEHOP, EMBOSSTranseq, ExPASyPROSITE, Genie, HMMSTR-ROSETTA-Server, InterProScan, ncbiblastn, ncbiblastp, Primer3, webcutter_2_0, WebLogoSequenceLogo

• SeqPad accepts all common sequence file formats, both via the build-in import function and via “Drag & Drop”.

e.g. FASTA DNA, FASTA Protein, Genbank, Genpept, Swissprot, EMBL DNA, EMBL Protein, Clustal W, MSF, BLAST XML, PDB,…

• Project & Workflow centric GUI
  • Tree view showing all project data: sequences, annotations, tasks…
  • Overview of all scheduled jobs (batch processing)
  • Project data saved as BioSQL compliant Schema

[ 2. Advanced Data Visualization]

SeqPad features an integrated visualization engine in order to represent both 2D sequence data and 3D molecule models (PDB-files).

• 2D Sequence Viewer

• Semantic Zooming & Multiple Color Schemes (SeqPad, Bioedit, Viseur, Rasmol)
• Graphical pairwise comparison of 2 sequences (“Dotplot”)
• Multiple Alignment viewer

• 3D Visualization

i. PDB Molecule Viewer with Multiple display types (Wire frame, Space fill, Balls & Sticks, Tube, Smooth Tube, ... )

1. Bi-directional 2D-3D Selection & Coupling (selected sequence fragments in the 2D viewer are highlighted in the 3D molecule viewer and vice versa)

Feature List (somewhat longer version)

[ 1. General Features]

1. SeqPad Project tree.

• Shows all project data in a hierarchically structured way.
• A project typically exists of several sequences, 3D structures, multiple alignments and external documents.
• The project data of each project is saved in a BioSQL compliant scheme.

2. DNA/Protein collections

• Projects can contain several collections. Each collection is either filled with DNA data or protein data.
• Unlimited numbers of collections can be added to the project.
• Switch between DNA and Protein with one simple click.

3. Graphical Sequence and Feature viewer and editor.

• Graphical representation of all the features, with graphical distinction between Range location, Between location and Point location features.
• The features have a user definable 'feature color scheme'.
• Bumping features: features are layed out so that they do not overlap.
• Semantic zooming: what kind of data and how much data is actually shown, depends on the level of zoom.
• Different color schemes for the sequence symbols: SeqPad, Bioedit, Viseur, Rasmol. All color schemes can be used as background or foreground coloring.
• Features can be added, edited or removed. When adding a feature you can choose from a list of over 600 predefined feature types, or define a new type.
• Color scheme based text editor with advanced search and replace options (e.g. PERL like regular expressions).
• Talk! Select any sequence or subsequence and let your computer tell you how it sounds.

4. Advanced 3D Molecule Viewer

• Several display types to choose from: Wire frame, Space fill, Balls & Sticks, Tube, Smooth Tube, ...
• Several color schemes: Element, Index, Amino, Chain, Segment or Structure based.
• Multiple light options
• Support for Zooming, Rotating, Panning, ...
• Support for Amino acid selection
• Hardware accelerated (Direct3D/OpenGL)

5. Session-based workflow control for your (remote) tasks.

• Possibility to remove tasks.
• Possibility to re-execute earlier executed tasks.

6. Real time view port

• The viewport lets you navigate in very large sequences or multiple alignments.
• With one click you can jump to the correct place in the sequence viewer.
• When scrolling through the sequence or alignment viewer, the viewport always tells you where you are currently located, how big the different sequences are and how they are layed out.

7. Unique Zoomable User Interface

• Semantic, vector-based zooming: no matter what level of zoom the viewer will always display meaningful information.
• LOD (Level of detail) support: the kind of data depends on the level of zoom.
• Massive number of options like: Fit-to-window, Zoom window, Zoom slider, Fish eye lens mode, Dynamic mouse zooming, ...
• Generic framework: every viewer in SeqPad automatically receives the same functionality. Even new, custom made, integrated viewers would get the zoomable user interface.
• Full screen mode support for all viewers

8. Link a 3D molecule with any sequence and/or phylogenetic tree

• Every 3D structure can be linked to any sequence and/or phylogenetic tree from your project.
• Select symbols or even features in the 2D sequence viewer and look at the corresponding selection in the 3D viewer!
• Select elements in the 3D viewer and immediately see the corresponding highlighted symbols in the Sequence Viewer!
• Slide through a phylogenetic tree and discover reserved regions in sequences and 3D viewer simultaneously

[ 2. Drag & Drop features]

• Easily integrate your existing (web-based) bioinformatics tools! The project panel accepts Drag & Drop operations from several locations as: HTML browser, File System Explorer, ...
• Automatic recognition of dropped biological files, including (but not limited to):
  • FASTA DNA
  • FASTA Protein
  • Genbank
  • Genpept
  • Swissprot
  • EMBL DNA
  • EMBL Protein
  • Clustal W
  • MSF
  • BLAST XML
  • PDB
• Possibility to Drag & Drop non biological, binary files. These will be added as external documents to your SeqPad Project and can be viewed from within SeqPad.

[ 3. Integration & Third party tools]

• NCBI BLAST. Submit any BLAST task in just 2 mouse clicks !
  When your result comes back from NCBI, look at it in our “Graphical BLAST viewer”
  and see things you might not have seen before..

• SeqPad integrates with several web-based bioinformatics tools.

Upon selection of sequence data, it automatically fills in the necessary data fields of the tool,
for easy submission of web-based tasks.

SeqPad provides a default (html template) integration after installation for:

• BDGP
• BDGPSplice
• ClustalW
• CODEHOP
• EMBOSSTranseq
• ExPASyPROSITE
• Genie
• HMMSTR-ROSETTA-Server
• InterProScan
• ncbiblastn
• ncbiblastp
• Primer3
• webcutter_2_0
• WebLogoSequenceLogo?
  '

[ 4. Advanced 3D molecule viewer]

SeqPad has a built-in PDB Molecule Viewer that supports multiple display types and advanced manipulation techniques:

· Smooth Tube

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· Sticks

· Tube

· Balls & Sticks

· Compound docking with visual docking indication, e.g. compound docking into pharmacophore (GAG sequence)

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[ 5. Multiple Alignment Viewer]

• Load multiple alignment files from a remotely executed 'multiple alignment'
  into the SeqPad multiple sequence viewer.
• Add or remove gaps yourself to optimize the alignment.
• While adding or removing gaps, all graphical features are still shown.

[ 6. Dotplot]

• Combine any two sequences from your project to produce a graphical pairwise comparison
• Change parameters like window size or threshold and watch the resulting plot change in real-time
• Use the 'color matrix' to produce a hot-to-cold-colour based multi-color shaded plot.

7. [ Phylogenetic tree viewer]

· Unrooted genome-wide tree, (log) transformed

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· Radial projection, (log) transformed

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· Inject discrete data, e.g. expression levels

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· Radial view annotated with discrete data: identifying gene clusters with similar expression = novel biological insight !

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[ 8. Sequence editor]

• Fast symbol text editor
• Different color schemes, with background or foreground coloring
• Advanced search and replace options (e.g. PERL like regular expressions).
• Insert or Overwrite mode

9. [ Sequence transformations]

• Several sequence transformations possible: Reverse, Complement, Reverse complement, Shuffle, Bisulfide.
• DNA to Protein translations
  • Graphical view of the six-frame translation
  • Forward or Backward translation

[ 10. Feature editor]

• Unlimited number of features can be added and removed.
• Existing features can be edited with the Feature Editor
• When creating or adding a feature you can choose from a list of over 600 predefined feature types,
  or define a new type.

[ 11. External documents]

• Any type of external files and documents can be added to your SeqPad Project
• Possibilities are Word/Excel/Powerpoint documents, HTML/PDF documents, Images, Animations, Movies, Sound clips, ...

[ 12. Freehand marking]

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• All SeqPad viewers offer the possibility to add freehand marks.
• Use freehand drawing mode to animate your SeqPad project presentations