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.