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5.3 years ago
vytarasov
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I would like to present here a program - BioLabDonkey - for molecular biologists who are Mac users. This program is written from scratch in a language native for Mac - Swift. The program can be downloaded from mac App Store - https://apps.apple.com/us/app/biolabdonkey/id1470827582?ls=1&mt=12 It is not free but it is definitely affordable for students. It is one time purchase app, no subscription. New features will be added regularly. The program has a following list of features:
- Opens files (for DNA, protein, alignment) with the extensions: .txt, .rtf, .fasta, .fas, .fa, .fsa, .ffn, .fna, .seq, .ape, .gb, .gbk, .ab1, .bldna, .fas, .faa, .seq, .gp, .blprotein, .pdb, .fastq, .aln, .blalignment, .jpg, .tiff, .png,
- Saves files (for DNA, protein, alignment) with the extensions: .txt, .rtf, .fasta .fas, .fa, .fsa, .ffn, .fna, .seq, .gb, .gbk, .ab1, .bldna, .fas, .faa, .seq, .gp, .blprotein, .blalignment, .pdf, .eps, jpg, png
- Transcribe, reverse complement and translate DNA sequence
- 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,
- View GC content, CpG islands and Stem Loops,
- Generate Plasmid, Linear map,
- Generate and edit DNA, protein features for genbank, genpept format files,
- Generate features database and perform automatic features annotation,
- Copy/paste the selected DNA sequence with features,
- Find DNA restriction sites and DNA fragments,
- Genome viewer,
- Virtual DNA gel,
- Multiple alignment and realignment of DNA and protein sequences,
- Phylogenetic tree,
- 3D Protein/DNA/RNA viewer,
- Prediction of protein secondary structures,
- Hydropathicity/pI plots,
- Limited proteolysis,
- Find protease sites and protein fragments,
- RNA-Seq DE - Genes and miRNAs differential expression,
- Calculator 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,
The site with BioLabDonkey Help Book is here - https://molbiolinfo.home.blog
Any question/advice is welcome!
The BioLabDonkey update - 1.3 - is released in Mac App Store with
The BioLabDonkey Version 1.4 is released with:
The BioLabDonkey Version 1.6 is released with:
I was asked to add to BioLabDonkey an option to read xdna files from Serial Cloner app. It looks right now, at academic institutions, there is a demand for a mandatory Catalina upgrade, to 64bit, and Serial Cloner is not compatible with this macOS. So I have made parser for xdna files and have made the following BioLabDonkey update :
BioLabDonkey Version 1.8 :
The BioLabDonkey Version 1.9 is released with:
Dear users, if there is a need for a new feature implemented in the program let me know here !
The BioLabDonkey Version 1.10 is released.
In a coming next version a new feature - assembly of reads from .ab1 (or .txt) files - will be added. This function is designed for not high number of reads and it is independent of read size.
The BioLabDonkey Version 2.0 is released.
Hi, I was wondering if it's possible to get a trial run or a detailed tutorial video so that I can understand if it's worth purchasing for my needs. I have used Serial Cloner for a long time and was quite happy with it until getting a new Mac... I don't want to use Snapgene so seriously considering buying this if it works fine. I'll also purchase for my group (10 members) but it all comes down to whether the app is what we need.
Looking forward to hearing from you!
Oz
Hi Oz, At Apple App Store there is no such a functionality as trial version. All tutorial materials (some small updates are missing) you can find at this website -
https://molbiolinfo.home.blog/biolabdonkey-features/
What is not there is a description for assembly function, this function is new and I will add the description soon. There is also one video, without sound, for the restriction analysis in BioLabDonkey. I plan to add more tutorial videos, for other functions.
Several month ago I have been asked by one head of the lab in University of Arizona a similar question about usage of BioLabDonkey instead of Serial Cloner. For his needs I have made parser for Serial Cloner xdna files and added several new features. You can ask him about his experience with BioLabDonkey. His webpage info - https://medicine.arizona.edu/person/michael-s-kuhns
And, if you would like to have some new features or improvements in BioLabDonkey I am always open to make them.
Best,
Valeriy
The BioLabDonkey Version 2.5 .
New feature - easy cloning of restricted DNA fragments with GenBank features in three clicks. In DNA1 (DNA2) Tab, select the restriction sites in the table, select the restricted fragment in the table and press the “DNA2” (“DNA1”) button to clone the fragment into the DNA sequence in DNA2 (DNA1) Tab.
New feature - a table with amino acid composition. Amino acids can be marked/unmarked in different colours.
There are options to choose the translation frames to display in the Text Map and to copy/paste a reverse strand of the selected DNA sequence with features.
The BioLabDonkey Version 2.9
New functionality from 2.6 to 2.9 version
Hi,
Like Oz, I have also been serial cloner user until Apple decided to stop 32-bit programs. Do you offer the capabilities to do virtual PCR, Gateway/recombination cloning? Not having trial version is such a bummer, can't just purchase a software that does not have extensive documentation/user base without having tried it.
Thank you for your work!
Santosh
Hi, there are no options for virtual PCR, Gateway/recombination cloning.
Frankly to say I don't see a sense in virtual PCR. From my experience with PCR in wet lab (more then 20 years) to have a good result of a real PCR you don't need virtual PCR, waste of time. It is just matter of choice of good primers and polymerase preset.
For the documentation you can visit website, it has the same content as HelpBook in the program.
The BioLabDonkey Version 3.0
New update of BioLabDonkey - Version 3.2
If somebody had a problem with opening .xdna or .dna file I hope in this version they are solved. If not, let me know.
Here is the link to new YouTube video tutorial for Version 3.2 -
Restriction Analysis and Cloning in BioLabDonkey (Plasmid, Linear and Text Maps) - part 1
Update of BioLabDonkey - Version 3.5, optimised for macOS Big Sur
Here is the link to the second part of YouTube video tutorial (Version 3.5) -
Cloning and GenBank features in BioLabDonkey (Plasmid, Linear and Text Maps) - part 2
Update of BioLabDonkey - Version 3.7
GenBank features, RevComplement/Transcribe/ Translate, Find Motifs and ORFs in BioLabDonkey - part3
Primers, DNA sequencing chromatogram, reads alignment and assembly in BioLabDonkey - part 4
A new tutorial for BioLabDonkey version 3.7
CG , CpG, Stem Loop content, Codon Optimisation and Silent Insertion/Deletion of Restriction Sites in ORF - part 5
Update of BioLabDonkey - Version 3.10 and two tutorials
Genome and Protein Tabs functionality in the BioLabDonkey - part 6
PDB viewer in the BioLabDonkey - part 7
Update of BioLabDonkey - Version 4.0
Update of BioLabDonkey - Version 5.2
Update of BioLabDonkey - Version 5.6