Blast2GO Previous Versions

Blast2GO Basic Maintenance Update

• Fix to prevent B2G files from becoming corrupted

• Improve GFF export functions
• Improve error handling on truncated GFF input
• Fix Extract Fasta from GFF feature hierarchy
• Improve GFF/GTF attribute detection
• Improve GTF gene structure visualization
• Fix KEGG objects save issue
• Improve GSEA memory handling
• Improve Workflows inputs/outputs handling
• Improve Generic Statistics side-panel
• Load TimeLogic file parsing improvements
• Minor Fixes

• Import Blast Results: minor bug fixes
• Workflows: minor bug fixes and improvements
• Kegg: memory optimizations
• GO Graphs: memory optimizations when exporting png
• InterPro Scan: improve progress communication
• NCBI Blast: improve communication in case of errors
• Create Count Table: memory and performance optimizations

• Venn Diagrams
• FastQ Pre-Processing (Adapters, Quality, Length)
• Workflows allow regular files as input and output
• Context Menu for GFF and VCF tables
• GSEA with “No Filter” option
• Minor bug fixes and improvements

• Improved Sequence Viewer
• Genome Browser performance improvements
• RNA-Seq De-Novo Assembly report improvements
• Changed colors for up(red)/down(green) regulated pairwise statistics
• KEGG with https connection
• Rfam connection improvements
• Minor bug fixes and improvements

• FastQ Quality Check
• RNA-Seq DeNovo Assembly
• Combined Genome Browser Visualization
• Support for Variant Call Format
• Merge Blast2GO Projects using the File Manager
• Interactive Heatmap from Pairwise Results
• Network License Support

• InterProScan in the Cloud (CloudIPS)
• Workflows (Create, View, Run)
• De-Novo Transcript Level Quantification (Fasta + FastQ)
• Blast Result Alignment Viewer
• High Performance GFF File Viewer
• PDF Reports for “RNA-Seq” and “Gene Finding” features
• New Gene Ontology ID-Mapping Strategy (faster, more complete, “gi” independent)
• New design for many result pages
• “Find Similar Sequences” performance improvements
• Faster Species Taxonomy Queries
• Preferences: Define Memory and Temporary Files Settings
• Preferences: Choose Gene Ontology Version: latest or month
• Improved “Cloud Usage” Monitor

• CloudBlast now for multiple Projects in parallel
• Prokaryotic GeneFinding (Glimmer): Improved Perform. and Report
• GO Graph Visualisation: Improved Filtering
• InterProScan: Improved Communication
• Rfam: Merge GOs to Projects
• BioMart: More Stable Data Retrieval
• Minor Bug Fixes

• RNAseq Read Count to Quantify Expression (BAM + GFF)
• Coding Potential Assessment (CPAT)
• New Result Table (side-panel, tags, colors, filters, context menu)
• Enrichment analysis now for ANY functional label
• Differential Expression Analysis with improved visualisations
• Faster Gene Finding
• Memory and CPU Monitor
• Improved “Extract Fasta” feature (GFF + Ref-Fasta)
• Improved GFF table to easily search and filter attributes

• Gene Finding: RNA-Seq Exon Support for Augustus
• Differential Expression Count Table: Improved format check
• GSEA enriched GO Gene-List export feature
• NCBI Blast: Improved application messages
• File Manager: Improved performance
• Minor Bug Fixes

• Differential Expression Analysis for Pairwise and TimeCourse
• Gene Finding for Eukaryotes and Prokaryotes
• Gene Set Enrichment Analysis (GSEA)
• ID and Sequences Conversion by: Extract Top Hit Sequences via Blast and Blat
• New App Manager now with Blast2GO “Featured” Apps
• Blast2GO Featured App: Create NCBI Submission Files
• New App: Ortholog Group Finder (COG/EggNOG)
• New Load and Export Functions: CountTable, GFF3 Object, ID-Value List, Generic Table
• New Organic Graph Layout
• Generic Table Column have now a (Un)Select All function
• We added Icons to the Load, Export and Context Menu
• Improved QBlast and Local Blast (now version 2.4) behaviour
• Improved Proxy Settings (now available via the activation dialog)
• Fixed InterProScan Bug with ORF prediction

• New BASIC feature: Easily create and blast against a local databases.
• New filters can be applied during the annotation step. These filters allow e.g. to easily perform a “Top-Hit-with-GOs” annotation.
• New feedback forms allows us to improve Blast2GO with the help of your input.
• The new Blast2GO App Manager allows to add additional tools to Blast2GO.
• Predict bacterial protein subcellular localization annotations with PSORTb 3.
• The “Translate longest ORF” feature has now many more options and allows you to choose the open reading frame based on the Top Blast Hit.
• Create distribution charts (dot, bar, line) of any of your generic table columns.
• Easily find and remove highly similar and/or redundant sequences within large datasets using the BLAT algorithm.

• Faster Gene Ontology Mapping in BASIC mode via web services (no direct mysql connection with an open network port 3306 needed).
• New interactive offline Gene Ontology graph visualisation.
• Blast results in new XML2 format for improved Gene Ontology Mapping and taxonomy information.
• Analysis history for all Blast2GO files.
• Improved Gene Ontology import for gene symbol, accession and GenBank ID lists.
• Improved InterProScan XML import.
• Merge Blast2GO datasets direclty from within the FileManager.
• Top Blast Hit export now available in the Generic Export function.
• Several new summary charts for the Gene Ontology Mapping and the InterPro step.

• Work with multiple datasets in paralell (PRO feature).
• Use the FileManager to organize your datasets and results.
• Save and reopen all analysis results like graphs, charts, enrichments, etc.
• Run RFAM analysis. Detect non-coding RNA, cis-regulatory elements or self-splicing RNAs (via EMBL-EBI webservice).
• WordCloud or Treemap viewer allow to summarize functional profiles.
• Extract FASTA sequences via GFF/GTF files.
• Extract subsets and ID list from your project.
• Customize your sequence table columns (e.g. remove columns you are not interested in).
• A new Fast-Blast option to speed-up your blast results.

• Blast2GO in a fresh new look.
• Many performance, design and user interface aspects have been improved.
• Progress bars, application messages and many other tools make working with Blast2GO now more efficient.

• Last release of the Blast2GO Java WebStart version.
• The development and maintenance/update of this version is now discontinued.