Sequence annotation

From MyBio

[edit] Categories which link here

• Sequences

[edit] Sequence annotation - Quick Links

GATU

[edit] Sequence annotation - Web Resources

Genome Annotation Transfer Utility (GATU) is a platform-independent (java-based) tool designed to efficiently annotate genomes based on a closely related reference genome that is already annotated. Unlike some other annotation tools, GATU does not require sequences to be aligned prior to file import. The program uses BLASTn and tBLASTn algorithms to map genes from the reference genome onto the new sequence. In addition, a NEEDLE alignment of the protein sequences is performed; similarity at both the nucleotide and amino acid level is considered. ORFs present in the target genome and absent from the reference genome are also identified, these can be further analyzed (using BLAST, VGO, BBB etc.) and then accepted or rejected for annotation. GATU can handle multiple-exon genes as well as mature peptides. The goal is to annotate the majority of the new genome's genes in a single run, making GATU ideal for large sequences. Although it was designed for use with large viral genomes, GATU can also be used to aid in the annotation of larger genomes (such as bacterial genomes). Files can be uploaded in FASTA or GenBank format.

Artemis Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, and is available for UNIX, GNU/Linux, BSD, Macintosh and Windows systems. It can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format.

GeneCluster 2.0 GeneCluster 2.0 expands the data analysis capabilities of GeneCluster 1.0 by adding supervised classification, gene selection and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-nearest neighbors (KNN) algorithms. It enhances the clustering capabilities of GeneCluster 1.0 by adding a module for batch SOM clustering, and also includes a marker gene finder based on a KNN analysis and a visualization module. It implements the methodology used in Golub et al. (1999) and Slonim et al. (2000). Requires JRE 1.3.1 (Java Runtime Environment).

DPL Forum: Too few categories!

Ensembl Bioinformatics framework to organize biology around the sequences of large genomes. Joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Bioinformatics framework to organize biology around the sequences of large genomes. Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on metazoan genomes. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. Ensembl is primarily funded by the Wellcome Trust.

Apollo Genome Annotation and Curation Tool Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment. It was used by the FlyBase biologists to construct the Release 3 annotations on the finished Drosophila melanogaster genome, and is also a primary vehicle for sharing these annotations with the community. The Generic Model Organism Database (GMOD) project, which aims to provide a complete ready-to-use toolkit for analyzing whole genomes, has adopted Apollo as its annotation workbench. Apollo is a Java application that can be downloaded and run on Windows, Mac OS X, or any Unix-type system (including Linux).

Ganesh Genome ANnotation for Expressed Seqeunce Tags.

GALA Genome Alignment and Annotation database. This database incorporates information about genes, SNPs, alignments, disease association and gene expression levels. Data is from multiple sources such as GenBank, Ensembl, The Whitehead Institute, and The Human Genome Browser.

GenePalette: Software for analysis of sequence features in genomic DNA Application enabling users to search a genomic regions for consensus matches visualizing their position in the context of intron-exon structure. Compatible with any genome sequence in genbank. Website has libraries for promoter prediction.

Babelomics Babelomics includes tools for functional annotation of pre-selected sets of genes, such as FatiGO+, Tissue Mining Tool and MARMITE. It also includes the FatiScan tool and an improved GSEA module to find blocks of functionally related genes.

<books></books>