PDB viewer in the BioLabDonkey – part 7
Genome and Protein Tabs functionality in BioLabDonkey – part 6
CG , CpG, Stem Loop content, Codon Optimisation and Silent Insertion/Deletion of Restriction Sites in ORF – part 5
Primers, DNA sequencing chromatogram, reads alignment and assembly in BioLabDonkey – part 4
GenBank features, Reverse-Complement/Transcribe/ Translate, Find Motifs and ORFs in BioLabDonkey – part 3
Cloning and GenBank features in BioLabDonkey (Plasmid, Linear and Text Maps) – part 2
New graphic view of BioLabDonkey user interface
The version 3.0 of BioLabDonkey is in macAppStore. It has new, clean graphic user interface. In the previous posts you can find the description of the BioLabDonkey functionality for old text based user interface. This description is correct for the new version except of the text based buttons are exchanged to the pictograms.
Important. The assembly can be efficiently performed for up to several hundreds reads, not more!
“open” button – opens files with extensions: .ab1, .abi, .txt.
“save” button – saves the selected contig consensus to file with .txt extension.
“delete” button – delete the selected read files in the files table.
“clear” button – delete all read files in the files table.
“print” button – use this button to print the assembly graphic map or to save it into pdf or eps file.
- Reads files table
- Assembly – graphic map, assembled reads, consensus and coverage
Reads files table
Press the “open” button to open a file or multiple read files (.txt, .abi, .abi). The file names will appear in the column “File Name”. To delete the files select the rows and press the “delete” button. To clear the files table press the “clear” button.
Assembly – graphic map, assembled reads, consensus and coverage
To start assembly select the minimal reads overlap value, then press the “assemble” button. Play with this value to get an appropriate result. To cancel assembly press the “cancel” button.
The assembly result will appear as a set of contigs in the contigs table. Select a contig in the table to see the assembly map. In the map each arrow represents a sequence file. The green arrow corresponds to an original file sequence, and the red arrow represents a reverse complement sequence. Click on an arrow to see the corresponding file in the files table.
For .ab1, .abi files a double click on the selected file row opens a new window with ABI chromatogram.
If the contig length is less than 3000 bp the reads sequences and consensus are displayed. For longer contigs click and drag on the assembly map to see the reads sequences and consensus in the corresponding region. To shift the view frame to the left or right side use the “<” and “>” buttons. To return to whole contig view use the “return” button.
Below the assembly map, each vertical red/green bars represents an assembly coverage for each nucleotide. The red bars mean nucleotide variations. On the assembly map these variations are displayed as vertical dash red lines. Place the mouse pointer over a bar to see the coverage number and the nucleotide variation. This functionality is available when the contig frame is less than 3000 bp.
Press the “save” button to save a contig consensus sequence to .txt file. To open a consensus sequence in the “DNA1”, “DNA2” or “Alignment” Tab press corresponding buttons.
Restriction Analysis and Cloning in BioLabDonkey (Plasmid, Linear and Text Maps) – part 1