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Showing posts with label Sequence analysis software. Show all posts

Showing posts with label Sequence analysis software. Show all posts

GenomeQuest - Sequence data management (SDM) platform

At the core of GenomeQuest is the GQ-Engine - a database engine that is purpose-built for storing, managing, and analyzing sequence data at NGS scale.

GenomeQuest is the world's leading sequence data management (SDM) platform. Researchers use state-of-the-art tools to store, manage, and analyze genomic data. Bioinformatics teams get a development platform to customize workflows, build applications, and unify their sequence data environment. IT and business managers can efficiently scale to NGS across discovery operations.

Science Applications
GenomeQuest provides cutting-edge computational, querying, and visualization tools along with applications that accelerate research and discovery.

Built-In Collaboration
A web-based dashboard offers easy access to everything your team needs - including compute resources, sequence datasets, and discovery tools.

High Performance Infrastructure
GenomeQuest is purpose-built for large-scale sequence data management and analysis, utilizing cloud-based, embarassingly parallel" computing.

Unified Database for all Sequence Data
Sequences

Software Link: GenomeQuest

DNAnexus - Sequence Data analysing software

DNAnexus provides solutions for both DNA sequencing centers growing their next-gen capacity, and researchers working with next-gen sequence data. Our web-based platform solves the data management and analysis challenges common to both with a single, unified system.

DNAnexus is built from the ground up to run on Amazon Web Services, the world's leading cloud computing provider. Our solution delivers not just software, but also all the computing and storage infrastructure. 100,000s of CPUs and 100s of petabytes of storage are available to you through DNAnexus, which acquires those resources on demand, allowing our pricing to mirror your usage. We support sequencing operations and research organizations of virtually any size, with absolutely no upfront hardware investment needed.

For core facilities with one instrument or sequence centers with 100 instruments, you can connect your sequencing output to DNAnexus in as little as 10 minutes. Learn more about what DNAnexus can do for your next-gen data management.

For researchers with a single lane of data, or for large commercial life science research organizations, DNAnexus can give you the right tools for your work, and the ability to scale up your research instantly in the future. Get started immediately without any setup or configuration.

Software Link: DNAnexus - Sequence Data analysis

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

SeqAssem - Contig Sequence Assembly Software

SeqAssem - Contig Sequence Assembly Software

Features:

View, edit and proofread DNA sequences and on-the-fly assembly of partial sequences into contigs
Imports files of the following formats: SCF 2.0, 3.0, ABI, AB1, FASTA.
Saves all information in small project files.
Shows estimation of total sequence quality (bad, intermediate, good).
Sorts sequences by quality, contig number, file name, ... or just arrange sequences by drag & drop.
Edit bases and compare with their peaks in the electropherograms.
Original trace data files are not altered.
Small-sized project files: electropherogram data is excluded from project files.
Restore original sequences by a single mouse click!

Software Link: SeqAssem - Contig Sequence Assembly Software

GeneStudio™ Pro - Sequence analysis software

GeneStudio™ Pro is a modern suite of molecular biology applications for the Windows platform built on our sequence format conversion engine, SeqVerter™. All manipulations with sequences of different formats are thus seamless and transparent for the user. In addition, GeneStudio™ Pro is very well integrated with the information available for molecular biologists on the Internet (please make sure to read the NCBI Disclaimer and copyright information before using Entrez and BLAST).

A convenient interface to Entrez allows the user to search GenBank® and retrieve sequences of choice directly into a sequence alignment or a contig assembly project.
BLAST searches can be done through a simple right click on a sequence or on a selected fragment of a sequence. BLAST results are retrieved and stored on the user's computer and can be viewed at any time.

GeneStudio™ Pro has an intuitive, user-friendly interface; most operations are done through drag-and-drop operations or through simple, uncluttered menus. In comparison to available command-line programs, Web-based utilities or programs accessed from a UNIX machine through an X-Windows interface, GeneStudio™ Pro can be mastered in a very short time.

Main changes in version 2.x:
The Alignment and Contig editors will now accommodate sequences longer than 500,000 bases and process them much faster than the previous versions.
Following suggestions from users, we included translation of sequences loaded into the Alignment editor as an aid in aligning sequences manually. Such mixed DNA/protein alignments may be saved in the new GSA format (*.gsa - GeneStudio Alignment).
Quality score of traces from Applied Biosystems DNA sequencers may be displayed as a visual aid to their quality,
Following the release of the new PHYLIP 3.6 package of programs for inferring phylogenies we offer the user the option to choose version 3.5 or 3.6.
Handling of the output of phylogeny programs was modified to give the user a choice to use the soon to be release GSTree (GeneStudio Tree) program instead of the TreeView tree display program.
All dialogs are now compatible with the East Asian versions of Windows.
GeneStudio Pro was compiled to be Unicode compatible.
GeneStudio Pro has a new look and feel of the visual components.

Software Link: GeneStudio™ Pro - Sequence analysis software

Genomic Software - Gapped SOLiD alignment analysis

The Omixon Gapped SOLiD Alignment plug-ins contain sequencer specific, highly accurate algorithms for reference based mapping, alignment and analysis. The Gapped SOLiD Alignment server and workbench plug-ins are intended for the analysis of color space data produced by Life Technologies SOLiD sequencers. Omixon plug-ins are designed to work with other high-throughput sequencing tools within the CLC Genomics Workbench.

Omixon offers a Gapped SOLiD Alignment plug-in for the CLC Bio Genomics Workbench and for the CLC Bio Genomics Server. The plug-ins provide Omixon's accurate SOLiD short read mapping and alignment expertise via the CLC bio platform.

User benefits
• Highest possible accuracy for short read NGS analysis.
• The lowest amount of unmapped or incorrectly mapped reads. Less wasted sequences and wasted consumables.
• Find more variants than your competitors from the same run.
• Automatic handling of lower quality bases without dismissing entire short reads or trimming.
• No need to run pre-filtering tools. Automatic re-calibration of quality scores is part of the alignment.
• No need to run post-alignment tools such as variant equivalents since these are automatically handled at alignment level.
• No need to learn a range of parameters. Most parameterization is handled automatically. The user needs to select sensitivity, maximum mismatches and gaps.
• High performance: save on computing resources since this analysis is faster than the Smith-Waterman based short read aligners.

Gapped SOLiD Alignment
The Omixon Gapped SOLiD Alignment plug-in is based on the Omixon Color Space Toolkit and the algorithms described in Csuros, Juhos, Berces "Fast Mapping and Precise Alignment of AB SOLiD Color Reads to Reference DNA" Springer Lecture Notes in Bioinformatics 6293:176-188, 2010. It was designed to analyze short read sequencing data obtained from Life Technologies SOLiD next generation sequencing (NGS) instruments.

In contrast to other short read mapping and alignment tools the Omixon algorithms were designed specifically for a particular sequencer, in this case the Life Technologies SOLiD sequencer and its data error model. The mapping uses a spaced seed technique with greedy extension to find the most likely location of the short reads on the reference. In such an alignment, reads are mapped to approximate genome positions, allowing for a pre-specified bound on sequence divergence that combines nucleotide mismatches, gaps, and sequencing errors. The precise alignment relies on a pair hidden Markov model framework, combining DNA sequence evolution models and sequencing errors (from read quality values).

The Omixon Gapped SOLiD Alignment plug-ins provide the highest accuracy and gives you the best chance to find the diagnostically or biologically important variant you are looking for. This CLC Genomics plug-ins are designed to work with the other High-throughput sequencing tools and plug-ins provided by the Workbench. You can use the SNP and DIP (indel) detection tools of the workbench to call variants from the aligned reads.

Precise Variant Detection
The comprehensive probabilistic model incorporates quality scores from the sequencer, and a DNA mutation model (including G/C content, transitions/transversions, and sequence divergence). This allows for statistical confidence measures with no ad-hoc alignment scoring or thresholds.

Software Link: Genomic Software - Gapped SOLiD alignment analysis

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

SeqVerter - Sequence analysis software

SeqVerter™ is a free sequence file format conversion utility by GeneStudio, Inc. SeqVerter encapsulates a small subset of the features offered by the GeneStudio™ Pro suite of programs. While the standalone SeqVerter is a simple dialog-based utility, the free SeqVerter component of the GeneStudio Pro suite adds sophisticated viewers and sequence formatting functions, including a viewer for automatic DNA sequencer chromatogram files (traces). SeqVerter 2.x is fully compatible with East Asian versions of Windows.

Software Link: SeqVerter - Sequence analysis software

TreeMe - Phylogenetic Trees Analysis Software

TreeMe - Visualization, Editing and Annotation of Phylogenetic Trees

Features:

Visualisation of large phylogenetic trees (>1000 OTUs)
Combine trees: unites bootstrap labels of several trees onto a single tree
Full access to each node: modify node caption, branch caption, branch width, branch length, etc.
Annotate internal nodes (cluster nodes, clusters)
Collapse, Expand and Flip clusters
Re-root trees by using an outgroup
Define and visualise tags, e.g. arrows, boxes, text labels, etc.
Automatic replacing of taxon abbreviations (e.g. GenBank accession numbers) by complete names (e.g. by species names) using tab-delimited replacement files (edited with Microsoft EXCEL).
Fast location of nodes by searching for node names or other properties
Edit trees: move nodes, delete internal nodes, ...
Add links to taxa (e.g. to GenBank) and jump to the sequence data with a single mouse click!
Clipboard functions: Copy tree and insert into other software (Word, Powerpoint, ...)
Printing of trees
Imports: NEWICK (Phylip, MrBayes), NEXUS (Paup), ...
Outputs: NEWICK (Phylip, MrBayes), NEXUS (Paup), Vector Graphics (EMF, Windows Enhanced Metafile).

Software Link: TreeMe - Phylogenetic Trees Analysis Software

DNA Dragon - DNA Sequence Contig Assembler Software

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

DNA Baser Assembler - DNA sequence analysis software

DNA Baser Assembler is unique and revolutionary bioinformatics software for manual and automatic DNA sequence assembly, DNA sequence analysis, automatic sample processing, contig editing, metadata integration, file format conversion and mutation detection. Its unbeatable price and the truly user-friendly interface makes DNA Baser the modern choice for DNA sequence alignment.

DNA Baser Sequence Assembler will do all the work for you. It will:

Automatically detect and trim low quality regions of your samples
Automatically trim vector sequences
Automatically correct the ambiguities in your contig
Automatically save the project and the contig to disk
With DNA Baser you will need literally 5 (five) seconds to go from unassembled samples ("dirty" samples with untrusted ends and vectors) to the final output data (the contig cleaned and saved to disk).

With DNA Baser Sequence Assembler, you can also:

Assemble multiple DNA samples or align to a reference sequence
Batch assemble or align groups of sequences by name (it will automatically recognize sequence pairs)
Import and analyze sequences from ABI, SCF, FASTA, SEQ, TXT, GBK
View and edit sequence traces
Mark specific regions (like discrepancies, low-quality areas in chromatograms) with visible colors and quickly navigate to these regions
Convert between different file formats (ABI, SCF, SEQ, FASTA, multi-FASTA, GBK...)
Automatically integrate metadata in all your contigs
Automatically detect and remove vectors

Software Link: DNA Baser Assembler - DNA sequence analysis

PersonalGenBank - Local sequence database software

PersonalGenBank is a database software maintaining sequences and sequence information in GenBank-format. Generally, the user downloads a large chunk of sequences from GenBank to the local computer and then imports these sequences into PersonalGenBank.

Sequence entries (the accession number) that are already present in the local PersonalGenBank-database are not imported except if the data deviates from existing data! In this case the old data is not overwritten but a new record is added to the database. The old record is marked as 'obsolete' in a special database field whereas the new record is marked as 'updated' plus a list of the deviating fields. This enables the user to quickly find updated records and to compare changes to previous data.

Import GenBank-formatted files into a database.

Filtering of incoming data (e.g. sequence motifs, taxonomic groups etc.).
Searching for records in the database.
Output the data as GenBank-formatted files.
Store the search and filter options in profiles.

Software Link: PersonalGenBank - Local sequence database software

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

GenomeTraveler - Genomics software

GenomeTraveler (GT) is a comprehensive software package for the analysis of whole genomes, which supports mapping of NGS fragments, mutation analysis, feature annotation and more.

Details

Key features of GenomeTraveler:
• Mapping of single- and paired-end fragments
• Contig mapping
• de novo assembly
• Import of mapping/assembling results from SAMtool, SOLiD, Velvet and Phrab
• Profile peak detection
• Mutation and SNP analysis
• Expression analysis
• The alignment viewer includes: search, annotation and comparative genome functions

GenomeTraveler is a program for next generation sequencing data analysis and annotation, which runs on Windows, Mac and Linux. It can handle data from Roche/454 GS FLX, ABI SOLiD and Illumina GA, and provides a graphical interface for smooth viewing and editing of mapping and assembly results.

The software runs on Windows, Mac and Linux and has been developed by in silico biology, Inc., in Yokohama, Japan. (http://www.insilicobiology.jp/en).

A free fully functional trial version, as well as further information, is available on our homepage.

Software Link: GenomeTraveler - Genomics software

Kodon - Sequence analysis software

In an era of total genome research and growing bioinformatics needs, Kodon embodies a new generation of desktop based sequence analysis software.

Running on industry leading database engines such as Oracle® and Microsoft® SQL ServerTM, Kodon is capable of handling extremely large databases, and can analyze full chromosomes or genomes with unparalleled power and speed. Every feature is designed for use in genome sequencing projects of any size.

Fully integrated environment for sequence analysis, including megabase assembly, vector cloning, ligation, primer design, alignment, homology search, match and repeat analysis, structure analysis, and much more
GenBank and EMBL are Kodon 's native formats. No conversion, no loss of features and qualifiers from documented sequences.
Storage and full analysis capability on local computers. No need to upload data over the Internet, avoiding network traffic, enhancing data security.
Automatic updates of databases from public servers; integrated BLAST, sequence download, Medline search etc.
Powerful chromosome comparison and gene annotation tools

Software Link: Kodon - Sequence analysis software

Pedant-Pro™ Sequence Analysis Suite

The Pedant-Pro™ Sequence Analysis Suite is a genome analysis package for comprehensive analysis of DNA and protein sequences. The software annotates individual sequences and entire genomes automatically, provides an easy-to-use interface for exploring genomic data and allows users to manually refine data for additional detail. The Pedant-Pro databases constitute a powerful and concise sequence, gene and protein repository - an ideal foundation for efficient research and development (R&D) processes. Cross-genome comparison (including positional linkage and phylogenetic profiling) extends the Pedant-Pro suite with tools for work in the industrial biotechnology sector.

Benefits for researchers:
Process large amounts of sequences with multi-method analysis in minimum time
Produce comparable results over numerous analyses
Simplify strain improvement using genome and pathway comparison
Find easily potential diagnostic and drug targets matching required properties
Add your own data: manually annotate gene functions, modify gene predictions, include experimental data and integrate proprietary databases
Visualize gene and protein properties using an easy-to-use graphical interface
Take advantage of expert knowledge and experience: use an optimized multi-method system without evaluating and managing the individual bioinformatic algorithms
Process entire method sets or subsets according to current requirements (e.g., perform exhaustive genome analysis or design your own workflow with protein domain analysis only)

Benefits for companies:
Enable optimal adaptation to the requirements of unique R&D processes through a dynamic workflow architecture: use standard workflows defined by Biomax scientists or specially design workflows for your projects
Save time and money in the sequence analysis process: use the high-throughput, industrial-scale Pedant-Pro grid-processing engine to analyze a maximum number of genomes, ESTs or other sequences in a minimum of time
Use the highly efficient EST pre-processing pipeline, streamlining the EST analysis process
Work with exactly the genomes you need: have your company or project-specific cross-genome comparison data set generated as a perfect basis for microbial analyses in industrial biotechnology.
Create a company-wide gene index with manual annotation functionalities for distributed systems, allowing all scientists of a project to access the active genomes easily
Save training time and money by providing an easy-to-use graphical user interface which allows efficient work for the bioinformatician as well as for the laboratory biologist from the first minute on

The Pedant-Pro Sequence Analysis Suite has been used at Biomax to annotate over 450 genomes in the PEDANT Genome Database.

Software Link: The Pedant-Pro™ Sequence Analysis Suite

Gene Inspector - Electronic Laboratory Notebook ELN

The Gene Inspector (GI) software program is a unique combination of a versatile electronic laboratory notebook, a comprehensive DNA and protein sequence analysis package, and a powerful illustration tool. The combination of an electronic research notebook with navigation and drawing tools, and sophisticated DNA and protein analyses, provides the ability to annotate experimental results and analyses in a single location, rather than keeping sequence analyses separate from experiment notes. The Gene Inspector software is available for both the Macintosh and Windows platforms, and files created on one can be shared across the other platform for easy collaboration. Gene Inspector allows users to organize large amounts of diverse, yet interrelated types of information - enabling researchers to plan, annotate, and carry-out molecular biology experiments and analyses in a truly innovative way.

Software Link: Gene Inspector - Electronic Laboratory Notebook ELN

BioNumerics Server - Sequence analysis software

BioNumerics Server has built and proven its reputation as the rock-solid and invaluable core of numerous public and private exchange, typing, and surveillance networks worldwide, of which the PulseNet initiative is undoubtedly the most prestigious example.

With BioNumerics Advanced Server, Applied Maths has combined all the existing client-server based connectivity and functionality with a new platform to build interactive, webbrowser-based services. Clients can connect to a BioNumerics Advanced Server from all over the world using their webbrowser and run queries, perform identifications, generate clusterings, or display phylogenetic trees within a web environment.

BioNumerics Advanced Server provides two solutions for sharing its databases and offering its services: a direct TCP/IP socket-based connection and a web-based communication. The socket-based connection is particularly designed for client-server platforms that include upload and download actions, whereas the web-based solution is suitable to provide services such as identifying unknown samples, placing an unknown sample in a dendrogram of database matches, assigning allelic and VNTR types, etc. Using the web-based functionality, the client does not need BioNumerics.

Software Link: BioNumerics Server - Sequence analysis software

Vector NTI - Sequence analysis software

Vector NTI® Advance software is the most highly integrated, multifunctional desktop sequence analysis application suite available today and provides superior integration, data management, and scalability.

Details

Vector NTI Advance® offers unparalleled, multi-modular, integrated sequence analysis and data management tools. The software contains a comprehensive set of data analysis and management tools, implemented across five application modules.

Detailed Pricing

$4,995 for a commercial license $2,998 for an academic license

Software Link: Vector NTI - Sequence analysis software

Lasergene Core Suite - Sequence analysis software

Lasergene Core Suite is a comprehensive DNA and protein sequence analysis software suite comprised of eight applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design. Lasergene Core Suite is available in four configurations, each designed with different researchers in mind. See the tabs below to find out which option best meets your needs.

The Lasergene Core Suite consists of all eight applications, and is the most robust of all the Lasergene Core Suite offerings. With the eight applications listed below, you can do sequence editing and map creation, contig assembly, multiple and pairwise alignments, design primers, discover genes, analyze and visualize protein structure, perform automated virtual cloning, and much, much more.
:

SeqBuilder - for sequence editing and annotation, automated virtual cloning, and primer design
SeqMan Pro- for contig assembly and analysis, including SNP discovery, coverage evaluation, and project annotation
MegAlign - for DNA and protein sequence alignments and analysis
GeneQuest - for gene discovery and annotation
Protean 3D - for exploring macromolecular structure, motion, and function
Protean - for protein structure analysis and prediction
PrimerSelect - for primer design
EditSeq - for importing and editing unusual file types

Software Link : Lasergene Core Suite - Sequence analysis software

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