Search Results for "Databases Open Source & DevTools"

Coati is a web development framework and API for genome databases that supports multiple database vendors and database schemas.

...A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124

VIGOR (Viral Genome ORF Reader) is a perl application to predict protein sequences encoded in viral genomes. VIGOR determines the protein coding sequences by sequence similarity searching against curated viral protein databases. Please see the wiki to see list of all supported viruses. This work has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services...

FIAP (Fully Integrated Annotation Pipeline) is a fast bacterial genome multithreading annotation pipeline written in Perl that detects genes coding for proteins, tRNAs, and rRNAs (5S, 16S and 23S). FIAP also allows users to include an infinite number of custom databases. This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows...

Primer prediction from alignments and consensus sequences. easyPAC applies all standard quality tests to degenerate primer and primer pairs and optionally maps all primer candidates to an arbitrary number of reference files like repeat databases or genomes to ensure target specifity.

Automated Sequence Annotation Pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible databases.

The Princeton Protein Orthology Database (P-POD), developed by the Genome Databases Group at Princeton, computes and displays families of orthologs between multiple organisms.

Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases. See http://bit.ly/bfirSh and http://bit.ly/bwpnSY for latest developments.

The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.

UniDPI stands for Unified Database of Protein Interactions which gives access to documented interactions in several independent and heterogeneous databases disseminated on the web.

A gene and protein homology database toolset that uses existing data from ensembl and entrezgene online databases.

TSE is a test bed for a web service approach to federating taxonomic name databases. Put in English, it takes your query and talks to a number of different databases, asking each one whether they contain that name.

HomGL is a web-based tool for comparing gene lists obtained e.g. by microarray studies. Unigene, Locus Link & Homology databases are used to compare gene lists with different accession numbers and between different organisms.

gbwget is a command line/screen oriented tool to search in nucleotide or protein databases and to view or retrieve database entries. It can easily integrated into the EMBOSS seqence analysis Suite can also be used standalone.