BioLabDonkey

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: 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.