Omixon Cloud Gate - Free Bioinformatic Software

In order to be able to process the very large bioinformatics files on the cloud, we have developed a utility to transfer files of up to 5 terabytes in size to and from S3. This utility takes advantage of the parallel transfer capabilities of S3 and can achieve very high speeds of data transfer, depending on the capability of the network used.

The utility can be used to upload data to the cloud, download data from the cloud, and transfer data to and from Amazon instances running on the cloud. It also includes support for HDFS (hadoop distributed file system). It can be used as a simple command line utility, or can be plugged in to your own applications.

Main features of Cloud Gate
• Completely free.
• A simple command line utility, written in Java.
• Also has a simple Java API, so can be integrated and used easily from within any Java application.
• Parallel data transfer, using the S3 multipart upload functions.
• File size of up to 5 terabytes.
• Upload and download between your local machines and S3.
• Transfer data between cloud-based instances and S3.
• Transfer data between HDFS (hadoop distributed file system) and S3.

Transfer speeds:
• Between cluster compute instances (with extra-fast networking) and S3 - up to 300 megabytes per second.
• Between standard Amazon instances and S3 - typically between 10 and 40 megabytes per second.
• Upload speed to the cloud (and download speed from the cloud) is effectively only limited by the capability of the internet connection used, up to a current maximum of 300 megabytes per second.

Software Link: Omixon Cloud Gate -  Free Bioinformatic Software

Read more

The Gene Construction Kit (GCK) program - Plasmid mapping software

The Gene Construction Kit® (GCK) program has been the preferred plasmid mapping software of leading researchers for more than 20 years. GCK allows easy manipulation of DNA sequences, either graphically or as sequence text - quickly saving users both time and money. GCK eliminates tedious examination of DNA sequence data by automatically identifying open reading frames (ORF's), keeping track of sticky ends during cutting and pasting of restriction enzyme digestion fragments, assisting with PCR primer design, and enabling comprehensive annotation of DNA sequence features. This DNA analysis software allows multiple files to be opened and displayed simultaneously, allowing DNA sequences to easily be copied and pasted between plasmids and vectors to represent real-world DNA cloning protocols. The Gene Construction Kit software is available for both Windows and Macintosh users, and files can be shared across platforms allowing for easy collaboration. The interface and set of functions in GCK will significantly enhance laboratory productivity and minimize experimental design errors - saving users both time and money.

Software Link: The Gene Construction Kit  (GCK) program - Plasmid mapping software

Read more

BioEdit - Sequence alignment program

BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by Tom Hall (North Carolina State University). It also provides BLAST  capability on local databases

Software Link: BioEdit - Sequence alignment program

Read more

PeakScanner - DNA fragment analysis software

The software allows you to view, edit, analyze, print, and export fragment analysis data generated using the Applied Biosystems Genetic Analyzers.

Details

Use this free software to perform DNA fragment analysis; separate a mixture of DNA fragments according to their sizes, provide a profile of the separation, and precisely calculate the sizes of the fragments. The software allows you to view, edit, analyze, print, and export fragment analysis data generated using the Applied Biosystems Genetic Analyzers.

• Use a workflow panel to guide you through analysis
• Quickly analyze samples with the default sizing methods
• View or print thumbnail and checkerboard view
• View raw and analyzed data simultaneously
• Analyze large fragments (e.g. 1200 bp)
• Get better results with linear and non-linear sizing algorithms

Easy to use
Peak Scanner™ Software v1.0 guides you through the process of fragment analysis. If you just want to quickly perform an analysis, you can use default analysis methods to get the answers you need. Having problems? Use the latest troubleshooting tools. The clear iconography and simple project archiving means this tool is the easiest way to perform DNA fragment analysis.

Customizable
Customize Peak Scanner™ Software v1.0 to streamline your process. Adjust thumbnail and checkerboard viewing and printing options; change the sample and sizing tables; edit locking and selective analysis, including peak labeling, merging and splitting. You can even overlay sizing curves on analyzed data.

Flexible
Peak Scanner™ Software v1.0 enables the simultaneous viewing of raw and analyzed data. Now you have the ability to size large fragments such as 1200 bp sized fragments.Use either linear or non-linear sizing algorithms. This flexible software tool has the potential to be used in many novel applications.

Looking for More Software Tools?
Visit our new Software Community Program for a list of data analysis and management software tools that enhance Applied Biosystems products.

Detailed Pricing

PeakScanner is free. 

Software  Link: PeakScanner - DNA fragment analysis software 

Read more

Methyl Primer Express - DNA methylation analysis software

This free software enables you to design high quality PCR primers for methylation mapping experiments. Simply cut and paste in your region of interest. The tool searches for CpG islands and simulates bisulfite modification of DNA in silico. Applied Biosystems supplies all the tools you need to complete methylation mapping experiments.

Methyl Primer Express® Software v1.0 enables you to:

• Easily design robust primers for methylation studies.
• Annotate the transcription start base and translation start codon.
• Highlight target regions of interest and examine these boundaries in your primer design reports.
• Predict CpG islands in your DNA sequence.
• Simulate the bisulfite modification of DNA.
• Create a reference" sequence for downstream sequencing analysis.
• Modify CpG Search and Primer Design Criteria Easily
• Flexible software enables you to easily modify the criteria you use to search for CpG islands in your sample DNA.
• Create Information-Rich Reports
• Create primer design reports containing your sample's initial DNA sequence 

Software Link: Methyl Primer Express - DNA methylation analysis software

Read more

ClustalX - Sequence alignment program

ClustalX is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results. . 

(Reference: J.D. Thompson et al. (1997). Nucleic Acids Research 24: 4876-4882).

Software Link ClustalX - Sequence alignment program

Read more