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

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Sequencher 5.0 - DNA sequence data anaylsing Software

Sequencher 5.0 from Gene Codes Corporation takes you from DNA sequence data to results easier and faster than ever! Over 20 years of daily use by biologists in labs around the world have refined Sequencher's tools and interface. You get the power and speed to get accurate results from your DNA analysis, and get back in the lab more quickly. Whether you need DNA sequence assembly and analysis tools for next-generation or traditional (Sanger or Capillary Electrophoresis) DNA data sets, Sequencher 5.0 will guide you toward results.

Next-generation DNA data sets:

• Maq and GSNAP alignment algorithms
• SNP analysis and methylation studies
• Tablet Viewer

Traditional DNA data sets:

• Multiple, configurable DNA Assembly algorithms
• Comprehensive DNA sequence editing tools
• Full support of sequence data confidence values

Next-generation or Traditional DNA data analysis features:

• Powerful reference sequence alignment
• Variance Table to discover SNPs quickly and easily
• Extensive data import and export capabilities
• NCBI BLAST search
• Forensic mtDNA profiling

Software Link:  Sequencher 5.0

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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

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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

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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

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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.

1. 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, ...).
2. Easy to use interface which accelerates the proofreading and the comparison of nucleotides with trace peaks.
3. XML-conform project files containing all necessary data.

Software Link:  DNA Dragon - DNA Sequence Contig Assembler Software

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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

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Geneious Server - Sequence analysis software

Geneious Server™ is an enterprise software package designed to put powerful software and hardware tools in the hands of everyday biologists to accelerate discovery.
Details
Geneious Server is a powerful server software package designed specifically for highly intensive computing.

From their desktop, Geneious Pro users can simply offload heavy data crunching to Geneious Server for faster analysis of large volumes of sequence data. The server's power and research data can be shared securely amongst teams of researchers. The result is dramatically faster analysis leading to more discoveries.

• The Benefits of Geneious Server:
• Speed up research
• Use open peer-reviewed algorithms
• Free up your desktop computer
• Share computing power within your team
• Harness all your computing resources
• Take advantage of acceleration technologies
• Securely access and share data

Software Link: Geneious Server - Sequence analysis software

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SequiLab - Sequence profiling portal

Sequilab is a sequence profiling portal that instantly connects the sequence data of a researcher to a host of sequence analysis tools from around the globe. It also has web2.0 feature built into it for researchers to collaborate and interact with each other.
Details
Sequilab is a sequence-profiling portal with web 2.0 interactivity features built into it. It allows the user to directly link NCBI-BLAST results instantly to an inventory of sequence analysis tools like translate, ORF, CpG islands, View structure (Cn3D), mfold (for RNA) without cutting and pasting. As a result, researchers can quickly get back to their bench without having to labor countless hours on Internet jumping across different sites.

In addition to the seamless integration of BLAST results with sequence analysis tools, Sequilab also allows users to

• Save the results of their research for later use
• Create custom toolbars of particular tools that are used most frequently.
• Instantly access latest feeds and content from top journals, job boards, seminars etc
• Create and manage their own Research Profile that highlights their experience in their field of work.
• Interact with other peers and professionals in the community forums.

By uniting sequence analysis research with social networking capabilities, Sequilab puts at the researcher's fingertips a powerful and expansive research productivity-enhancement tool that can save vast amounts of research time, reduce the potential for error, and unite pools of talent across the globe.

Software Link: SequiLab - Sequence analysis Software

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