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GenoList - An Integrated Environment for the Analysis of Microbial Genomes

GenoList - An Integrated Environment for the Analysis of Microbial Genomes | bioinformatics-databases | Scoop.it

To start using GenoList, you should first Select Organisms of interest, among the 743 genomes available in GenoList.

To this end, use the  button in the left-hand section of the current page.


Alternatively, using the "User Panel" just below, you can  (you should  first to create an account) in order to permanently store yourorganism(s) of interest.

Then, you can define Lists of Organisms, with three different Roles ("Query", "Comparative", "Favorite"), as explained in the Organism Selection page.


 

 



References:

  • SubtiList Bacillus subtilis strain 168 GenoList browser
  • Colibri Escherichia coli strain K12 GenoList browser
  • TubercuList Mycobacterium tuberculosis strain H37Rv GenoList browser
  • Leproma Mycobacterium leprae strain TN GenoList browser
  • BoviList Mycobacterium bovis strain AF2122/97 GenoList browser
  • BuruList Mycobacterium ulcerans strain Agy99 GenoList browser
  • ListiList Listeria monocytogenes strain EGD-e and Listeria innocua strain CLIP 11262 Multi-GenoList browser
  • LegioList Legionella pneumophila Paris strain and Legionella pneumophila Lens strain Multi-GenoList browser
  • PyloriGene Helicobacter pylori strains 26694 and J99 Multi-GenoList browser
  • MypuList Mycoplasma pulmonis strain UAB CTIP GenoList browser
  • CyanoList Synechocystis PCC6803 and Anabaena PCC7120 Multi-GenoList browser
  • AureoList Staphylococcus aureus strains N315 and Mu50 Multi-GenoList browser
  • StreptoPneumoList Streptococcus pneumoniae strains R6 and Tigr4 Multi-GenoList browser
  • SagaList Streptococcus agalactiae strain NEM316 GenoList browser
  • PhotoList Photorhabdus luminescens strain TT01 GenoList browser
  • CandidaDB


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GeneNest gene indices - EST clustering and assembly

GeneNest gene indices - EST clustering and assembly | bioinformatics-databases | Scoop.it

GeneNest is a comprehensive visualization of gene indices of the following organisms. The aim of GeneNest is to represent each gene by a single cluster of ESTs and/or mRNAs. Further subdivision of a cluster into contigs may be caused by alternative splicing, genomic sequences, or artefacts like chimeric sequences. Consensus sequence derived from GeneNest contigs are a basis for mapping genes onto the genome, and for analysis of splice isoforms (spliceNest).


Related tools:

SYSTERS

spliceNest


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GeneLoc Database

GeneLoc Database | bioinformatics-databases | Scoop.it

GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links toGeneCardsNCBI's Human Genome SequencingUniGene, and mapping resources. (More about GeneLoc.) 

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Rice Proteome Database

Rice Proteome Database | bioinformatics-databases | Scoop.it

REFERENCES:

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Geisha — a Chicken Embryo Gene Expression Database

Geisha — a Chicken Embryo Gene Expression Database | bioinformatics-databases | Scoop.it

GEISHA is the online repository of in situ hybridization and corresponding metadata for genes expressed in the chicken embryo during the first six days of development. GEISHA is a public resource funded by the National Institutes of Health, USA.


Access gene expression information in the following ways:


  • Use Browse to view information according to embryo stage, anatomical location, gene name or ID, citation keyword, or by multiple parameters

  • Use QuickSearch to query by gene name, anatomical 
    location, embryo stage, GEISHA ID, citation keyword, Gene ID, 
    or Gene Ontology keywords.

  • Use Gene Family QuickSearch to rapidly access information about genes that have regulatory functions during development.


Chicken Genome Browsers


Chicken EST Resources


Additional Genomic Resources

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FunShift — a Database of Pfam Subfamilies and Functional Shift Analysis

FunShift — a Database of Pfam Subfamilies and Functional Shift Analysis | bioinformatics-databases | Scoop.it

FunShift provides Functional shift (divergence) analysis between the subfamilies of a Protein domain family. The present release uses Protein Domain families in Pfam (Version 12.0).


Each family was divided into Subfamilies, after which Rate Shifting Sites (RSS) and Conservation Shifting Sites (CSS) were identified between each pair of subfamilies containing at least 4 sequences. The RSS and CSS values were used to predict if the function is shifted between the subfamilies.


This Resource provides:

  • Subfamily classification and alignments for each protein domain family.
  • Rate Shifting Sites for each pair of Subfamilies.
  • Conservation Shifting Sites for each pair of Subfamilies.
  • Prediction of Function shift between subfamilies for each pair.


Browse Families:

Numbers DUF A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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FunCoup - Networks of functional couplings/associations

FunCoup - Networks of functional couplings/associations | bioinformatics-databases | Scoop.it
Networks of functional couplings, or functional associations, inferred from high-throughput data and gold standards derived from protein complexes, physical interactions, metabolic pathways and signaling pathways.
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Infevers - a registry of Hereditary Auto-inflammatory Disorders Mutations

Infevers - a registry of Hereditary Auto-inflammatory Disorders Mutations | bioinformatics-databases | Scoop.it
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Drosophila RNAi Screening Center

Drosophila RNAi Screening Center | bioinformatics-databases | Scoop.it
DRSC provides bioinformatics tools, RNAi libraries, genome engineering reagents, cell screen protocols, etc. for Drosophila research.
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FlyBase - a database for drosophila genetics and molecular biology

FlyBase - a database for drosophila genetics and molecular biology | bioinformatics-databases | Scoop.it

FlyBase (http://flybase.org) is the leading website and database of Drosophila genes and genomes. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophilabiological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for. Here, we demonstrate some of our more advanced searching systems and highlight some of our new tools for searching the wealth of data on FlyBase. The first section explores gene function in FlyBase, using our TermLink tool to search with Controlled Vocabulary terms and our new RNA-Seq Search tool to search gene expression. The second section of this article describes a few ways to search genomic data in FlyBase, using our BLAST server and the new implementation of GBrowse 2, as well as our new FeatureMapper tool. Finally, we move on to discuss our most powerful search tool, QueryBuilder, before describing pre-computed cuts of the data and how to query the database programmatically.


LINKS

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3D-footprint: a database for the analysis of sequence recognition in protein-DNA complexes of known structure

3D-footprint: a database for the analysis of sequence recognition in protein-DNA complexes of known structure | bioinformatics-databases | Scoop.it
3D-footprint is a database of DNA-binding protein structures that is updated weekly with Protein Data Bank complexes, providing: interface graphs and footprint diagrams, structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, downloads, stats, complex of the week, a tutorial, an interactive footprint, a consensus miner
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FLIGHT - a Drosophila RNAi screen database

FLIGHT - a Drosophila RNAi screen database | bioinformatics-databases | Scoop.it

FLIGHT is an online resource compiling data from over 100 Drosophila in vivo and in vitroRNAi screens. FLIGHT includes details of RNAi reagents, and their predicted off-target effects, alongside RNAi screen hits, scores and phenotypes (including images and movies for high-content screens). 


This new release of FLIGHT is designed to enable users to upload their own RNAi screen scores and normalize them in a number of ways using the cellHTS2 R-package. Users can view quality control plots, detect and assign screen hits and compare hits from multiple screens, using a variety of methods including hierarchical clustering. FLIGHT integrates RNAi screen data with microarray gene expression as well as genomic annotations and genetic/physical interaction datasets. Indeed, the database also includes microarray gene expression profiles for over 20 Drosophila cell lines. 

FLIGHT is freely available for public use, however registering with FLIGHT will enable you to access additional functionality, including saving and combining gene lists, and submitting your own dataset for statistical analysis using cellHTS2.

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Modomics - A Database of RNA Modifications

Modomics - A Database of RNA Modifications | bioinformatics-databases | Scoop.it

MODOMICS and RNApathwaysDB are two complementary resources whichpresent RNA metabolism at different levels. While MODOMICS presents RNA modification pathways on the level of nucleosides, RNApathwaysDB deals with RNA metabolism with respect to whole RNA molecules. Our ultimate goal is to integrate these databases, however at the moment the users are invited to consult both of these complementary resources, depending on their needs and interests.


RNA databases

Auxiliary databases and tools

Ontology

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GeneTide Database

GeneTide Database | bioinformatics-databases | Scoop.it

GeneTide is an automated system for human transcripts (mRNA & ESTs) annotation and elucidation of 
 de-novo genes. (
More about GeneTide.)

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GeneAnnot Database

GeneAnnot Database | bioinformatics-databases | Scoop.it

GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBankRefSeq 

and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match. Where such matches are not found, probe-sets are annotated by their relation to GenBank mRNA sequences and UniGene clusters. The results are integrated with the GeneCardsGeneLoc and 

GeneNote databases.

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Gemina - a Genomic Metadata for Infectious Agents Database

Gemina - a Genomic Metadata for Infectious Agents Database | bioinformatics-databases | Scoop.it

Gemina is a web-based system designed to identify infectious pathogens and their representative genomic sequences through selection of associated epidemiology metadata. Gemina supports the development of DNA signature-based assays for the detection of pathogens or sets of pathogen through the Insignia Signature Pipeline at the University of Maryland. View the Quick Start or the Gemina Tutorial for help on searching the database.



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FunSimMat — a Functional Similarity Matrix

FunSimMat — a Functional Similarity Matrix | bioinformatics-databases | Scoop.it

FunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (PfamSMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). 


There are several search options available:

Disease candidate prioritization:

  • Rank candidate proteins using any OMIM disease entry
  • Compare a list of proteins to any OMIM disease entry
  • Compare all human proteins to any OMIM disease entry

Functional similarity:

  • Compare one protein / protein family to a list of proteins / protein families
  • Compare a list of GO terms to a list of proteins / protein families

Semantic similarity:

  • For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values.
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FungiDB - an integrated genomic and functional genomic database for the kingdom Fungi

FungiDB - an integrated genomic and functional genomic database for the kingdom Fungi | bioinformatics-databases | Scoop.it
FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. In its first iteration (released in early 2011), FungiDB contains the genomes of 18 Fungi covering 17 species. (see below). FungiDB integrates whole genome sequence and annotation and will expand to include experimental data and environmental isolate sequences provided by the community of researchers. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.
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FlyView - a Drosophila image database

FlyView - a Drosophila image database | bioinformatics-databases | Scoop.it

FlyView is the beginning of an image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes).The concept of FlyView includes compatibility to FlyBase, the main Drosophila database. 

Our aim is to establish the possibilty to compare images on the computer screen and to search for special patterns at different developmental stages. Therefore, all images are accompanied by text descriptions that can be used for searching.


FlyMove 

FlyBase 
Flybrain
Interactive Fly 

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FlySNP - a Drosophila SNP database

FlySNP - a Drosophila SNP database | bioinformatics-databases | Scoop.it

The FlySNP project aims to provide the information and technical resources to support high-throughput positional cloning in Drosophila melanogaster. These resources include a high-density genome-wide map of single nucleotide polymorphisms (SNPs), and inexpensive, high-throughput assays for SNP genotyping.

 

The specific aims were as follows:

 

1. To establish a map of >2200 SNP marker loci in the Drosophila genome.
These SNP markers have been identified in several commonly used genetic strains. The FlySNP project identified SNP markers within the sequenced, euchromatic regions of the X, 2nd and 3rd chromosomes. The average distance between SNPs is about 50 kb.

 

2. To establish robust, high-throughput assays for SNP genotyping.
Assays have been established using PCR, microarray and mass-spectrometry methods. The tag-array mini-sequencing (TAMS) approach has proven to be an especially fast and reliable method for SNP genotyping.

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Flybrain - an Online Atlas and Database of the Drosophila Nervous System

Flybrain - an Online Atlas and Database of the Drosophila Nervous System | bioinformatics-databases | Scoop.it
Flybrain provides an online atlas and database for anatomical images of and online publications about the Drosophila nervous system.
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FlyAtlas to identify better Drosophila melanogaster models of human disease

FlyAtlas to identify better Drosophila melanogaster models of human disease | bioinformatics-databases | Scoop.it

FlyAtlas, a new online resource, provides the most comprehensive view yet of expression in multiple tissues of Drosophila melanogaster. Meta-analysis of the data shows that a significant fraction of the genome is expressed with great tissue specificity in the adult, demonstrating the need for the functional genomic community to embrace a wide range of functional phenotypes. Well-known developmental genes are often reused in surprising tissues in the adult, suggesting new functions. The homologs of many human genetic disease loci show selective expression in the Drosophila tissues analogous to the affected human tissues, providing a useful filter for potential candidate genes. Additionally, the contributions of each tissue to the whole-fly array signal can be calculated, demonstrating the limitations of whole-organism approaches to functional genomics and allowing modeling of a simple tissue fractionation procedure that should improve detection of weak or tissue-specific signals.

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FLJ Human cDNA Database

FLJ Human cDNA Database | bioinformatics-databases | Scoop.it


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