We can also ligate fragments using the ligate button.Also, to create new PCR based fragments or synthetic adaptors. We can use either the graphics window or the text-based site usage windows, which makes it very easy to quickly extract a sub-sequence in a selection or in any restriction sites.There is a web browser tool within the software to allow direct import of NCBI and EMBL.Sequence features are visible on the sequence map.They can be automatically found by using the scan feature. Features can be manually entered or imported.The fully graphical map makes it easy to extract and select a fragment or even show single, double, or multiple cutters in a single window.All the tools required to analyze the sequence and modify if any changes needed are available in a single window making it very easy to use.The software comes with a high-quality graphics display and has a very user-friendly interface to the front end, which makes the interface very intuitive. They are processed both in sequence and as a graphic map. Since version 2.0 of the software, it also handles Annotations and features. It can read and write files in several formats, making it portable across multiple users who use different Molecular Biology tools. It is available free for download and can be used across multiple Operating Systems, including Windows, Mac, and Linux. Great for mutagenesis studies.Serial Cloner is a Molecular Biology Tool which is a front end to help with DNA Cloning, Sequence Analysis, and Visualization. Not only does it perform 2D alignments, but it also allows the user to see the position residues in the 3D protein sequence. This great piece of software from NCBI is a sequence viewer with a difference. A great all-round tool.Ĭn3D… say it out loud… “see in 3D”. ApE can be used for sequence annotation, restriction mapping, primer design, and sequence alignment. Sequences can be uploaded to ApE manually, directly from the NCBI database, or from ABI chromatogram traces. No scientist should be without this!ĪpE is an all-in-one plasmid and sequence workbench. Lab Assistant helps you organize your experiments with sticky “to-do” lists, timers, a calendar, and a lab journal. Actually, I’m not sorry because this is yet another GREAT piece of software from these guys. I’m sorry, this is yet another application from Mekentosj. PDF skim allows you to annotate a PDF file with your own notes and the makers hope that it will reduce the need for printing out PDF files. I’m cheating here slightly because I have mentioned PDF skim in another article recently, but it can’t be left out of this list. Geneious is a software package of genome & proteome research tools for protein, DNA, or molecular visualization, literature searching and storage…and more. Another piece of brilliant software from Mekentosj and a bargain at only 29 euros ($40). From the Papers interface, Pubmed searches can be performed and PDF files, complete with all metadata can be downloaded. Papers is an application for retrieving, archiving and viewing PDF files. This one is not actually free but is very cheap for the job it does. It has over a hundred preset compounds, which can be added to. This handy little application calculates the molecular weight of a molecule from its empirical formula. It’s miles better than any of its clunky counterparts… try it, you’ll love it! Serial Cloner is a fantastic all-in-one workbench import and manipulate sequences, construct plasmid and restriction site maps, determine %GC and fragment TM, extract and ligate fragments, perform virtual PCR… and lots more, all in one window using a very intuitive graphical interface.ĤPeaks is an extremely user-friendly DNA sequence chromatogram viewer and editor from the extremely talented guys at Mekentosj. If you are a PC user, click here for the PC list. If any of your favorite free programs are not included, please email me and I’ll add them or you can leave a comment with a link. I hope you will find at least some of it useful. I’ve put together this list of 10 pieces of free molecular biology software for Macs.
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