Life Science Software

Showing posts with label DNA analysis software. Show all posts

Align - Manual DNA sequence alignment editor

Alignment of DNA sequence, RNA sequence, protein sequence and other data
Imports and exports various sequence file formats, e.g. Paup-Nexus, Phylip, Fasta, EMBL, GenBank, DCSE, and others.

Features:

Find/Highlight sequence motives in your molecular sequence alignment (including wildcards ? or *)
Wizard for automatic processing of sequence alignments for phylogenetic analyses
Define phylogenetic masks: Which sites are good for phylogenetic analysis?
Select/Deselect sequences and save selection profiles to define subsets.
Sort sequences by: accession numbers, taxonomy, arrangement in a phylogentic tree and others
Several cursor shapes: normal, exclusive (edits all sequences except cursor position), ex- and insertional, left-ended cursor
Change the cursor to edit several sequences simulataneously
Analyze sequences and alignments: similarities, p-distances, RASA, ...
Manipulate aligned sequences: Translate DNA/RNAs to protein using your own codon usage table
Cut aligned sequences: e.g. remove common positions, where a mask sequence contains special characters
Create sequences: e.g. consensus sequences, frequency of characters, sites that are only present in selected species (signatures), ...
Full access to all GenBank fields
Batch replacement of accession numbers by other fields in foreign files, e.g. replace labels in a tree file. This is not necessary if you have TreeMe.
... and many other features.

Software Link: Align - Manual DNA sequence alignment editor

0 comments

GelQuest is the software of choice for the analysis of DNA fingerprint data and DNA fragment analysis. It works in a fast and efficient way with trace files (FSA files) as well as with gel image files (TIFF, JPG, BMP, etc.) and handles AFLP, t-RFLP, ERIC-PCR, RFLP-PCR or RAPD data.

For a detailed description of GelQuest software visit the features page. Just download a trial version to see how easy it works. The registration process is easy: just click the registration menu and order your license key!

Software Link: GelQuest - Software for the analysis of DNA fingerprints

0 comments

DNA Dragon Contig Assembler assembles sequences (FASTA, GenBank etc.), trace data (ABI, SCF, AB1), and Illumina and Roche 454 flowgrams into contigs. It is a very fast and accurate DNA sequence assembly software for MS Windows (c) operating systems. The DNA sequences are assembled into contigs and a direct comparision of trace date with nucleotide data is possible. It also allows for proofreading and base editing.

Fast and robust assembly machine handles more than 100000 samples from sequence formats (FASTA, GenBank, EMBL, etc.), trace file formats (SCF, ABI, AB1) and next generation sequencing file formats (Illumina, SFF, GFF, ...).
Easy to use interface which accelerates the proofreading and the comparison of nucleotides with trace peaks.
XML-conform project files containing all necessary data.

Software Link: DNA Dragon - DNA Sequence Contig Assembler Software

0 comments

3DNA is a versatile package for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures, based on a standard reference frame (Olson et al., J. Mol. Biol. 313(1), 229-237, 2001). In its core, the software uses a simple, yet mathematically rigorous and geometrically sensible, scheme for calculating a complete set of local base-pair, step, and helical parameters, and allows for exact rebuilding of a structure based on these parameters. Unique features of 3DNA include automatic classification of a dinucleotide step as A-, B-, or TA-like based on the positioning of the phosphorus atoms, and the generation of "standardized" base stacking diagrams. The rebuilding routines give Calladine-Drew style schematic representations of DNA as well as full atomic models with the sugar-phosphate backbone.

3DNA was created by Dr. Xiang-Jun Lu in the laboratory of Professor Wilma K. Olson at the Department of Chemistry and Chemical Biology, Rutgers-the State University of New Jersey. Since leaving Rutgers, Dr. Lu has continued to work on this project as an independent consultant in his spare time. This updated website provides users with more background information and technical details about 3DNA, including working examples. Thus, those who are really interested in nucleic acid structures can have a clear understanding of "what's going on in that black box".

3DNA has benefited greatly from interactions with the Nucleic Acid Database (NDB) project led by Professor Helen Berman. Dr. Zukang Feng at the PDB/NDB, Dr. A. R. Srinivarsan, Ms. Yurong Xin, Mr. Andrew Colasanti, Mr. Jin Tao, Ms. Fei Xu and other members of the Olson lab., and numerous users from around the globe have helped in making 3DNA a better tool to serve the scientific community.

This site has been tested to work on Windows 2000/XP running IE v5.0/6.0 and NetScape 7.2, RedHat Linux running Mozilla v1.4, and Mac OS X running IE v5.1 and Safari. It does not work on SGI running NetScape v4.7. Please let us know if have any problem with other OS/browser combinations.

Software Link: 3DNA - Analysis/ Rebuild/ Visualize of three-dimensional of DNA

0 comments

An exceptional tool for drawing publication and vector catalog quality plasmid maps, carrying out restriction analysis and designing cloning experiments.

Draw Exceptional Publication Quality Plasmid Maps

Whether you are a catalog company selling engineered plasmids or are performing restriction analysis for recombinant cloning experiments, SimVector will help you simulate the experiments and create publication quality plasmid maps from start to finish. Use the software to draw circular and linear plasmid maps in a variety of colors, patterns, fonts and line types. Display enzyme names in two font styles with the bacterium portion in Italics, as is traditional. Use even more than one font style and color in a single textual word anywhere in the plasmid map including in the feature annotations.

Export plasmid maps in EPS format for Adobe Illustrator 10, SVG for Microsoft Power Point 2002 or as ready-to-host web pages. Choose JPEG, TIFF and PNG formats for export.

Multiple Cloning Site (MCS) Display is Unique to SimVector

Vector catalogs generally display MCS's in a unique format, with enzymes one above the other in a vertical list. SimVector identifies the MCS's by interpreting GenBank header annotations or you can specify them manually. It then draws them in this special format we call the "Bracket View". It even has the smarts to list only the enzymes that cut within the MCS and nowhere else..

Lightning Fast Cloning Simulation

SimVector transforms annotations in sequence headers from GenBank or local files into fully illustrated maps. The cloning wizard steps you through popular recombinant protocols, such as Gateway® cloning and TA cloning, as well as one and two enzyme restriction cloning. ORF search helps you ensure that the construct remains in-frame. With a click of a button, you can translate sequences of expressed proteins to check for possible reading frame errors. With SimVector, cloning simulation is as simple as clicking a few buttons.

Restriction Analysis

SimVector has a comprehensive restriction enzyme analysis functionality. Choose from a database of more than a thousand restriction enzymes or use a popular commercial enzyme set we have preloaded. SimVector also enables you to construct your own custom enzyme sets.

Biologist-designed Intuitive Interface

SimVector has an intuitive biologist-designed interface to perform restriction cloning and sequence analysis. Point-and- click wizards make it easy to use even for beginners, while versatile functionality offers full control to experts for drawing plasmid maps.

Software Link: SimVector - DNA Cloning designing Software

0 comments

QuickGene is a molecular biology program for DNA analysis, assembly and cloning. We scientists deserve decent, modern software that doesn't require manuals or training courses to learn to use and that's where QuickGene comes in.

Details
Introducing the world's first intelligent and friendly genetics software.

QuickGene is a molecular biology program for DNA analysis, assembly and cloning. We scientists deserve decent, modern software that doesn't require manuals or training courses to learn to use and that's where QuickGene comes in.

Built by scientists for scientists, its goal is to be exceedingly user-friendly and intuitive, while making no sacrifices in functionality and incorporating all necessary functions in a single application.

regular updates keep QuickGene up-to-date
We're constantly working to make this a reality, introducing new features every month. QuickGene aims to be the absolute best while remaining affordable to everyone and constantly improving!

explore great new ways to create, visualize and share your research.
QuickGene already tackles all the basics of sequence analysis and introduces a number of great improvements.
The clean, tidy interface provides extensive sequence information exactly when and where you need it as well as offering the best search tool available. Fly through schematic sequence maps with navigation tools similar to those found in Google Maps and leave your enzyme catalogs on the shelf, as all restriction enzyme and buffer information is kept up-to-date!

save time & money with smart innovation
You can easily communicate your ideas from within QuickGene and we love to read and discuss every suggestion. Only with feedback will we be able to reach our goal of creating the best software to date with all the features you need. Your help is instrumental in this process!

Software Link: QuickGene - Molecular Biology Software