Software

ASAP

ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data collected by or in collaboration with researchers at the University of Wisconsin - Madison.

---

Base-by-Base

Base-By-Base is a whole genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows the user to easily navigate large alignments of similar sequences. Although Base-By-Base was intended as an editor and viewer for alignments of highly similar sequences, it is also provides many of the functions of other generic alignment editors. Comments and primer annotations can be added to the sequence. It allows various searches of the DNA sequences and may also be used for protein sequences.

---

Exonerate

Exonerate is a generic tool for pairwise sequence comparison. Support for many alignment models is available, using either exhaustive dynamic programming or a variety of heuristics to improve speed without compromising accuracy. Exonerate is used to generate transcript-based predictions in an EnsEMBL gene build (using the est2genome alignment model).

---

GATU

Genome Annotation Transfer Utility (GATU) annotates a genome based on a closely related reference genome. The proteins/mature peptides of the reference genome are BLASTed against the genome to be annotated to determine if they are present in the target genome. GATU has been tested on viral and bacterial genomes, it can correctly annotate the majority of the target genome's genes in a single step. GATU also flags potential genes in the target genome that are not present in the reference genome. The user has total control over, and selects, which genes should be annotated through an easy to use GUI; GATU writes a GenBank file as output. The program is intended for use by the bench scientist.

---

GraphDNA: DNA Skew Graphing

DNA Grapher allows the user to generate graphical representations of raw DNA sequences. To date, there are 8 graphing options (purine, keto, AT, GC, AC, GA, GT, TC skews; DNA Walks) and the user can plot genes or genomes from several file formats.

---

GUS

The Genomics Unified Schema (GUS) is an extensive relational database schema and associated application framework designed to store, integrate, analyze and present functional genomics data. The GUS schema supports a wide range of data types including genomics, gene expression, transcript assemblies, proteomics and others. It emphasizes standards-based ontologies and strong-typing.

---

GUS WDK

The GUS Application Framework offers an object-relational layer and a Plugin API used to rapidly create robust data loading programs for diverse data sources. The GUS distribution includes plugins for standard data sources. The GUS Web Development Kit (WDK) is a rich environment for efficiently designing sophisticated query-based websites with little programming required. The GUS WDK is designed to accelerate the creation of "data mining" websites. It can work on any relational database system and on any schema. See www.plasmodb.org (version 5.0 or later) and www.cryptodb.org for sites created with it.

---

Genewise

Genewise compares a protein sequence or protein profile HMM to a DNA sequence. For protein-centric gene prediction, such as the EnsEMBL, Genewise represents the main predictor of gene structures. The code has many parameters to improve the discrimination and accuracy of the final prediction. The wise2 package contains gene frequency files for human and worm sequences so for use with other eukaryotic species you will need to restrict splice sites to the canonical GT..AG or make new training tables. A non-spliced option exists for working with prokaryotic species.

---

JDotter

Java-Dotter (JDotter) is an interactive platform-independent Java interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization.

---

JIPS

Java GUI for InterProScan (JIPS) is a graphical user interface for finding new motif/domains/fingerprints in repeated InterProScan searches. JIPS compares results from InterProScan searches performed with two versions of an InterPro database and highlights new motifs/Domains/fingerprints that are from the updated database. Results are displayed in an easy-to-use tabular format. JIPS also contains tools to assist with ortholog-based comparative studies of protein signatures.

---

Manatee

Manatee is a web-based gene evaluation and genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments using a multitude of genome analyses tools. These tools consist of, but are not limited to GO classifications, BER and blast search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee is funded by The National Institute of Allergy and Infectious Diseases (NIAID) as part of the NIAID Bioinformatics Resource Centers (BRC) for Biodefense and Emerging or Re-Emerging Infectious Diseases.

---

Mauve

Mauve constructs global multiple alignments of rearranged genome sequences. It also provides an interactive display of multi-species sequence conservation and any annotated features in those genomes. It can be applied for sequence comparison of both finished or incomplete genomes in multiple contigs. The resulting display is useful for identifying functional chromosomal regions under selective pressure and for performing ortholog assignment based on conserved gene order. Mauve writes out global alignments in eXtended Multi-FastA (XMFA) format, a phylogenetic guide tree in Newick format, and the location of genomic islands. It identifies the breakpoints of genomic rearrangement and can provide a reduction of the genomes to a signed permutation matrix suitable for inference of rearrangement history.

---

MUMmer

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

---

SEED

The SEED is a genome Annotation/Analysis tool designed to support comparative analysis of genomes. The system is commonly used to: study a specific subsystem (set of genes), support community-wide annotation of genomes, and search for specific missing genes.

---

Sybil

Sybil is a web-based software package for comparative genomics. It was developed by the Bioinformatics department at The Institute for Genomic Research (TIGR) and is funded by The National Institute of Allergy and Infectious Diseases (NIAID) as part of the NIAID Bioinformatics Resource Centers (BRC) for Biodefense and Emerging or Re-Emerging Infectious Diseases. The primary goal of the Sybil software package is to supply online comparative analysis tools for the Pathema web site (a Bioinformatics Resource Center located at TIGR), which will provide in-depth curatorial and comparative analysis of several pathogens.

---

VGO

Viral Genome Organizer (VGO) is a java based interface for viewing and analyzing genomes (or any DNA sequence). It can be used to display a variety of information including genes, ORFs, nucleotide composition and start/stop codons. It can also be used to perform a regular expression search, a fuzzy motif search, and a genome search with Mass-spec data. Since VGO makes use of the VBRC VOCs database, it allows the user to identify related genes in multiple genomes. It is useful for genome annotation.

---

VOCs

Viral Orthologous Clusters (VOCs) is a Java based user interface for a genome database. NIH funded databases contain complete genomes of Arena-, Bunya-, Flavi-, Filo-, Toga-, Paramyxo- and Pox- viridae for public access. Other funding supports Adeno-, Asfar-, Baculo-, Corona-, Herpes-, Irido-viridae databases. VOCs allows users to easily search a database for protein sequences or genes of a known function or for a specific genome and then apply different analysis techniques to the search result. VOCs provides quick and easy access to tools do BLAST searches, Multiple Sequence Alignments, DNA/protein dotplots, and genome statistics. A key feature is the grouping of orthologs in families, so that the user can easily manipulate data at the gene/protein, ortholog family or genome level.

---

Workflow

Organizations have process piplelines that need to be created, executed, and monitored on an on-going basis. Each pipeline may include multiple discrete process that can be executed either sequentially or in parallel. To reduce manual intervention, and streamline the process flow, IGS's software team has designed a system called Workflow that can be used to build, run, and monitor such process pipelines or workflows. WorkFlow is funded by The National Institute of Allergy and Infectious Diseases (NIAID) as part of the NIAID Bioinformatics Resource Centers (BRC) for Biodefense and Emerging or Re-Emerging Infectious Diseases.