BioLabDonkey
macOS / Education
This program is aimed at researches in the molecular biology field for use in their everyday routine work. It is a suite of the bioinformatic tools for the analysis of DNA, RNA, and protein sequences, as well as images of gels, blots, cells and colonies. It also provides a set of useful calculators for molecular biology.
The user interface was developed around a minimalistic design and ease of use, such as: direct access to functions in less than three clicks, essential functionality with a minimum of settings, minimisation of windows (uncluttered screen). The user can resize, maximise the window as well as open the multiple windows.
The program includes custom algorithms for: the protein/DNA sequences alignment, protein secondary structures prediction, RNA-seq differential expression.
Features:
- Open files with the extensions: .txt, .rtf, .fasta, .fas, .fa, .fsa, .ffn, .fna, .seq, .ape, .gb, .gbk, .embl, .ab1, .bldna, .xdna, .dna, .faa, .seq, .gp, .blprotein, .fastq, .aln, .phylip, .blalignment, .pdb, .jpg, .tiff, .png.
The program reads files created by Serial Cloner(.xdna), DNA Strider(.xdna), SnapGene(.dna) and ApE (.ape) programs.
- Save files with the extensions: .txt, .rtf, .fasta, .fas, .fa, .fsa, .ffn, .fna, .seq, .gb, .gbk, .embl,.ab1, .bldna, .faa, .seq, .gp, .blprotein, .blalignment, .pdf, jpg, png;
- Transcribe, reverse complement and translate DNA sequence;
- Tm, %GC, Mw, length of selected DNA and protein Mw (average and monoisotopic), length of protein, amino acid composition, protein net charge;
- Find open reading frames (ORFs);
- Find sequence motifs (repeats, palindromes, stem loops and arbitrary sequences) in DNA sequence;
- Generate primers;
- View ABI sequencing chromatogram, edit sequence;
- Generate ORF silent mutations;
- Optimize codons in ORF;
- View GC content, CpG islands and Stem Loops;
- Generate Plasmid, Linear and Text map using feature annotations from genbank file;
- Generate and edit DNA/protein features for genbank/genpept format files;
- Generate DNA features database and perform features annotation;
- Copy/paste the selected DNA sequence with features;
- Cloning of a restricted DNA fragment;
- Find/highlight DNA restriction sites and DNA fragments;
- Genome viewer;
- Virtual DNA gel;
- In-silico PCR;
- Multiple alignment and realignment of DNA/RNA/protein sequences;
- Assembly of sequencing reads from .ab1 or txt files;
- Phylogenetic trees;
- Protein/DNA/RNA PDB viewer;
- Prediction of protein secondary structures;
- Reverse translation;
- Protein Hydropathicity/pI plots;
- Protein limited proteolysis;
- Find/highlight protease sites and protein fragments;
- RNA-Seq DE: genes and miRNAs differential expression;
- Calculators for: Dilution, Molarity, Ligation, SDS PAG, Ammonium sulfate, Bacteria growth;
- Nucleic acid OD conversion;
- Units conversion for DNA and protein;
- Colonies/Cells/Spots counting;
- Analysis of Gel/Blot photo and calculation of relative fold-change in selected Gel/Blot bands/spots;
- Image adjustment and labels.
Quoi de neuf dans la dernière version ?
* When calculating the gel/blot band density ratios:
1) the user can select a row in the table as a new reference density band and press the calculation button – the app will recalculate the ratios relative to the selected value.
2) the user can select the rows in the table and copy the row values by two finger click on touchpad to paste after as a text in a Text Editor or as a table in Keynote.
